B7-Like Molecules and Uses Thereof

ABSTRACT

The present invention provides B7-Like (B7-L) polypeptides and nucleic acid molecules encoding the same. The invention also provides selective binding agents, vectors, host cells, and methods for producing B7-L polypeptides. The invention further provides pharmaceutical compositions and methods for the diagnosis, treatment, amelioration, and/or prevention of diseases, disorders, and conditions associated with B7-L polypeptides.

This application claims the benefit of priority from U.S. ProvisionalPatent Application No. 60/233,867, filed on Sep. 20, 2000, thedisclosure of which is explicitly incorporated by reference herein.

FIELD OF THE INVENTION

The present invention relates to B7-Like (B7-L) polypeptides and nucleicacid molecules encoding the same. The invention also relates toselective binding agents, vectors, host cells, and methods for producingB7-L polypeptides. The invention further relates to pharmaceuticalcompositions and methods for the diagnosis, treatment, amelioration,and/or prevention of diseases, disorders, and conditions associated withB7-L polypeptides.

BACKGROUND OF THE INVENTION

Technical advances in the identification, cloning, expression, andmanipulation of nucleic acid molecules and the deciphering of the humangenome have greatly accelerated the discovery of novel therapeutics.Rapid nucleic acid sequencing techniques can now generate sequenceinformation at unprecedented rates and, coupled with computationalanalyses, allow the assembly of overlapping sequences into partial andentire genomes and the identification of polypeptide-encoding regions. Acomparison of a predicted amino acid sequence against a databasecompilation of known amino acid sequences allows one to determine theextent of homology to previously identified sequences and/or structurallandmarks. The cloning and expression of a polypeptide-encoding regionof a nucleic acid molecule provides a polypeptide product for structuraland functional analyses. The manipulation of nucleic acid molecules andencoded polypeptides may confer advantageous properties on a product foruse as a therapeutic.

In spite of the significant technical advances in genome research overthe past decade, the potential for the development of novel therapeuticsbased on the human genome is still largely unrealized. Many genesencoding potentially beneficial polypeptide therapeutics or thoseencoding polypeptides, which may act as “targets” for therapeuticmolecules, have still not been identified. Accordingly, it is an objectof the invention to identify novel polypeptides, and nucleic acidmolecules encoding the same, which have diagnostic or therapeuticbenefit.

SUMMARY OF THE INVENTION

A novel polypeptide, which is related to proteins in the T-cellcostimulatory pathway, has been identified. This polypeptide, termedB7-like polypeptide (B7-L), represents a B7-related polypeptide having astructure similar to and sharing homology with CD80, CD86, B7RP-1, andB7-H1. Human B7-L polypeptide shares a greater amino acid identity withhuman B7-H1 (35%) than with other members of the B7 family (B7rp-1, 20%;B7-1, 12%). In addition, the mouse and human orthologs of B7-Lpolypeptide and B7-H1 share a greater degree of amino acid similarity(approximately 70%) than the mouse and human orthologs of B7-1, B7-2, orB7rp-1 (approximately 40%). Furthermore, both B7-H1 and B7-L bind to thesame receptor, PD-1.

The present invention relates to novel B7-L nucleic acid molecules andencoded polypeptides.

The invention provides for an isolated nucleic acid molecule comprisinga nucleotide sequence selected from the group consisting of:

(a) the nucleotide sequence as set forth in SEQ ID NO: 1;

(b) the nucleotide sequence of the DNA insert in ATCC Deposit No. PTA2481;

(c) a nucleotide sequence encoding the polypeptide as set forth in SEQID NO: 2;

(d) a nucleotide sequence that hybridizes under at least moderatelystringent conditions to the complement of the nucleotide sequence of anyof (a)-(c); and

(e) a nucleotide sequence complementary to the nucleotide sequence ofany of (a)-(c).

The invention also provides for an isolated nucleic acid moleculecomprising a nucleotide sequence selected from the group consisting of:

(a) a nucleotide sequence encoding a polypeptide that is at least about70 percent identical to the polypeptide as set forth in SEQ ID NO: 2 orthe nucleotide sequence of the DNA insert in ATCC Deposit No. PTA 2481,wherein the encoded polypeptide has an activity of the polypeptide setforth in SEQ ID NO: 2;

(b) a nucleotide sequence encoding an allelic variant or splice variantof the nucleotide sequence as set forth in SEQ ID NO: 1, the nucleotidesequence of the DNA insert in ATCC Deposit No. PTA 2481, or thenucleotide sequence of (a);

(c) a region of the nucleotide sequence of SEQ ID NO: 1, the nucleotidesequence of the DNA insert in ATCC Deposit No. PTA 2481, or thenucleotide sequence of (a) or (b) encoding a polypeptide fragment of atleast about 25 amino acid residues, wherein the polypeptide fragment hasan activity of the polypeptide set forth in SEQ ID NO: 2, or isantigenic;

(d) a region of the nucleotide sequence of SEQ ID NO: 1, the nucleotidesequence of the DNA insert in ATCC Deposit No. PTA 2481, or thenucleotide sequence of either (c) or (d) comprising a fragment of atleast about 16 nucleotides;

(e) a nucleotide sequence that hybridizes under at least moderatelystringent conditions to the complement of the nucleotide sequence of anyof (a)-(d); and

(f) a nucleotide sequence complementary to the nucleotide sequence ofany of (a)-(d).

The invention further provides for an isolated nucleic acid moleculecomprising a nucleotide sequence selected from the group consisting of:

(a) a nucleotide sequence encoding a polypeptide as set forth in SEQ IDNO: 2 with at least one conservative amino acid substitution, whereinthe encoded polypeptide has an activity of the polypeptide set forth inSEQ ID NO: 2;

(b) a nucleotide sequence encoding a polypeptide as set forth in SEQ IDNO: 2 with at least one amino acid insertion, wherein the encodedpolypeptide has an activity of the polypeptide set forth in SEQ ID NO:2;

(c) a nucleotide sequence encoding a polypeptide as set forth in SEQ IDNO: 2 with at least one amino acid deletion, wherein the encodedpolypeptide has an activity of the polypeptide set forth in SEQ ID NO:2;

(d) a nucleotide sequence encoding a polypeptide as set forth in SEQ IDNO: 2 that has a C- and/or N-terminal truncation, wherein the encodedpolypeptide has an activity of the polypeptide set forth in SEQ ID NO:2;

(e) a nucleotide sequence encoding a polypeptide as set forth in SEQ IDNO: 2 with at least one modification selected from the group consistingof amino acid substitutions, amino acid insertions, amino aciddeletions, C-terminal truncation, and N-terminal truncation, wherein theencoded polypeptide has an activity of the polypeptide set forth in SEQID NO: 2;

(f) a nucleotide sequence of any of (a)-(e) comprising a fragment of atleast about 16 nucleotides;

(g) a nucleotide sequence that hybridizes under at least moderatelystringent conditions to the complement of the nucleotide sequence of anyof (a)-(f); and

(h) a nucleotide sequence complementary to the nucleotide sequence ofany of (a)-(e).

The present invention provides for an isolated polypeptide comprising anamino acid sequence selected from the group consisting of:

(a) the amino acid sequence as set forth in SEQ ID NO: 2; and

(b) the amino acid sequence encoded by the DNA insert of ATCC DepositNo. PTA 2481.

The invention also provides for an isolated polypeptide comprising anamino acid sequence selected from the group consisting of:

(a) the amino acid sequence as set forth in SEQ ID NO: 3, optionallyfurther comprising an amino-terminal methionine;

(b) an amino acid sequence for an ortholog of SEQ ID NO: 2;

(c) an amino acid sequence that is at least about 70 percent identicalto the amino acid sequence of SEQ ID NO: 2 or the amino acid sequenceencoded by the DNA insert of ATCC Deposit No. PTA 2481, wherein thepolypeptide has an activity of the polypeptide set forth in SEQ ID NO:2;

(d) a fragment of the amino acid sequence set forth in SEQ ID NO: 2 orthe amino acid sequence encoded by the DNA insert of ATCC Deposit No.PTA 2481 comprising at least about 25 amino acid residues, wherein thefragment has an activity of the polypeptide set forth in SEQ ID NO: 2,or is antigenic; and

(e) an amino acid sequence for an allelic variant or splice variant ofthe amino acid sequence as set forth in SEQ ID NO: 2, the amino acidsequence encoded by the DNA insert of ATCC Deposit No. PTA 2481, or theamino acid sequence of any of (a)-(c).

The invention further provides for an isolated polypeptide comprising anamino acid sequence selected from the group consisting of:

(a) the amino acid sequence as set forth in SEQ ID NO: 2 with at leastone conservative amino acid substitution, wherein the polypeptide has anactivity of the polypeptide set forth in SEQ ID NO: 2;

(b) the amino acid sequence as set forth in SEQ ID NO: 2 with at leastone amino acid insertion, wherein the polypeptide has an activity of thepolypeptide set forth in SEQ ID NO: 2;

(c) the amino acid sequence as set forth in SEQ ID NO: 2 with at leastone amino acid deletion, wherein the polypeptide has an activity of thepolypeptide set forth in SEQ ID NO: 2;

(d) the amino acid sequence as set forth in SEQ ID NO: 2 that has a C-and/or N-terminal truncation, wherein the polypeptide has an activity ofthe polypeptide set forth in SEQ ID NO: 2; and

(e) the amino acid sequence as set forth in SEQ ID NO: 2 with at leastone modification selected from the group consisting of amino acidsubstitutions, amino acid insertions, amino acid deletions, C-terminaltruncation, and N-terminal truncation, wherein the polypeptide has anactivity of the polypeptide set forth in SEQ ID NO: 2.

The invention still further provides for an isolated polypeptidecomprising the amino acid sequence as set forth in SEQ ID NO: 2 with atleast one conservative amino acid substitution selected from the groupconsisting of: valine at position 4; isoleucine or valine at position 6;leucine or valine at position 7; methionine or valine at position 8;isoleucine at position 10; leucine or valine at position 17; glycine atposition 19; serine at position 22; leucine at position 23; asparticacid at position 28; leucine or valine at position 31; valine atposition 32; isoleucine at position 40; leucine at position 50; valineat position 52; valine, leucine, or methionine at position 55; arginineat position 61; methionine at position 62; lysine at position 70; serineat position 74; isoleucine or methionine at position 75; valine atposition 76; aspartic acid at position 78; methionine or isoleucine atposition 80; arginine at position 84; leucine at position 89; asparagineat position 91; isoleucine or leucine at position 92; isoleucine orleucine at position 94; glutamic acid at position 96; aspartic acid atposition 97; phenylalanine at position 100; valine at position 104;leucine at position 105; arginine at position 107; tyrosine at position110; glutamic acid at position 111; valine or isoleucine at position115; serine at position 116; valine at position 117; glycine at position121; valine or methionine at position 126; valine or isoleucine atposition 131; isoleucine or leucine at position 139; isoleucine atposition 141; serine at position 146; phenylalanine at position 148;isoleucine, methionine, or leucine at position 153; isoleucine atposition 160; threonine at position 165; aspartic acid at position 171;phenylalanine at position 174; serine at position 177; threonine atposition 178; valine at position 180; methionine, valine, or isoleucineat position 182; arginine at position 183; lysine at position 188;isoleucine or leucine at position 193; lysine at position 200; valine atposition 202; isoleucine at position 204; valine or methionine atposition 209; isoleucine at position 213; isoleucine or valine atposition 222; valine at position 223; leucine at position 225; valine orleucine at position 227; leucine or valine at position 231; leucine atposition 232; valine or leucine at position 235; methionine orisoleucine at position 240; arginine at position 250; arginine atposition 255; glutamic acid at position 256; serine at position 264;arginine at position 266; and leucine at position 268; wherein thepolypeptide has an activity of the polypeptide as set forth in SEQ IDNO: 2.

Also provided are fusion polypeptides comprising B7-L amino acidsequences.

The present invention also provides for an expression vector comprisingthe isolated nucleic acid molecules as set forth herein, recombinanthost cells comprising the recombinant nucleic acid molecules as setforth herein, and a method of producing a B7-L polypeptide comprisingculturing the host cells and optionally isolating the polypeptide soproduced.

A transgenic non-human animal comprising a nucleic acid moleculeencoding a B7-L polypeptide is also encompassed by the invention. TheB7-L nucleic acid molecules are introduced into the animal in a mannerthat allows expression and increased levels of a B7-L polypeptide, whichmay include increased circulating levels. Alternatively, the B7-Lnucleic acid molecules are introduced into the animal in a manner thatprevents expression of endogenous B7-L polypeptide (i.e., generates atransgenic animal possessing a B7-L polypeptide gene knockout). Thetransgenic non-human animal is preferably a mammal, and more preferablya rodent, such as a rat or a mouse.

Also provided are derivatives of the B7-L polypeptides of the presentinvention.

Additionally provided are selective binding agents such as antibodiesand peptides capable of specifically binding the B7-L polypeptides ofthe invention. Such antibodies and peptides may be agonistic orantagonistic.

Pharmaceutical compositions comprising the nucleotides, polypeptides, orselective binding agents of the invention and one or morepharmaceutically acceptable formulation agents are also encompassed bythe invention. The pharmaceutical compositions are used to providetherapeutically effective amounts of the nucleotides or polypeptides ofthe present invention. The invention is also directed to methods ofusing the polypeptides, nucleic acid molecules, and selective bindingagents.

The B7-L polypeptides and nucleic acid molecules of the presentinvention may be used to treat, prevent, ameliorate, and/or detectdiseases and disorders, including those recited herein.

The present invention also provides a method of assaying test moleculesto identify a test molecule that binds to a B7-L polypeptide. The methodcomprises contacting a B7-L polypeptide with a test molecule todetermine the extent of binding of the test molecule to the polypeptide.The method further comprises determining whether such test molecules areagonists or antagonists of a B7-L polypeptide. The present inventionfurther provides a method of testing the impact of molecules on theexpression of B7-L polypeptide or on the activity of B7-L polypeptide.

Methods of regulating expression and modulating (i.e., increasing ordecreasing) levels of a B7-L polypeptide are also encompassed by theinvention. One method comprises administering to an animal a nucleicacid molecule encoding a B7-L polypeptide. In another method, a nucleicacid molecule comprising elements that regulate or modulate theexpression of a B7-L polypeptide may be administered. Examples of thesemethods include gene therapy, cell therapy, and anti-sense therapy asfurther described herein.

In another aspect of the present invention, the B7-L polypeptides may beused for identifying receptors thereof (“B7-L polypeptide receptors”).Various forms of “expression cloning” have been extensively used toclone receptors for protein ligands. See, e.g., Simonsen and Lodish,1994, Trends Pharmacol. Sci. 15:437-41 and Tartaglia et al., 1995, Cell83:1263-71. The isolation of a B7-L polypeptide receptor is useful foridentifying or developing novel agonists and antagonists of the B7-Lpolypeptide signaling pathway. Such agonists and antagonists includesoluble B7-L polypeptide receptors, anti-B7-L polypeptidereceptor-selective binding agents (such as antibodies and derivativesthereof), small molecules, and antisense oligonucleotides, any of whichcan be used for treating one or more disease or disorder, includingthose disclosed herein.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1B illustrate the nucleotide sequence of the human B7-L gene(SEQ ID NO: 1) and the deduced amino acid sequence of human B7-Lpolypeptide (SEQ ID NO: 2). The predicted signal peptide (underline) andtransmembrane domain ( double underline) are indicated;

FIGS. 2A-2C illustrate an amino acid sequence alignment of human B7-Lpolypeptide (GA16817596; SEQ ID NO: 2), human CD80 or B7-1 (Cd80_Human;SEQ ID NO: 4; GenBank accession no. P33681), human CD86 or B7-2(Cd86_Human; SEQ ID NO: 5; GenBank accession no. U04343), human B7-H1(B37-H1_Human; SEQ ID NO: 6; GenBank accession no. AF177937), hum anB7rp-1 (B7rp-1_Human; SEQ ID NO: 7; GenBank accession no. AF199028),human PRO352 (Pro352_Human; SEQ ID NO: 8; GenBank accession no. Y41705),human butyrophilin BTF1 (Btf1_Human; SEQ ID NO: 9; GenBank accession no.U90543), human butyrophilin BTF2 (Btsf2a2_Hu; SEQ ID NO: 10; GenBankaccession no. U90550), human butyrophilin BTF4 (Btf4_Human; SEQ ID NO:11; GenBank accession no. U90546), human butyrophilin BTF3(Btn3a3_Human; SEQ ID NO: 12; GenBank accession no. U90548), andbutyrophilin (Btn_Human; SEQ ID NO: 13; GenBank accession no. U39576);

FIGS. 3A-3E illustrate a portion of the genomic nucleotide sequence forhuman B7-L polypeptide (SEQ ID NO: 14). The location of the deducedamino acid sequence of exon 1 (SEQ ID NO: 19) is indicated.

FIG. 4 illustrates a portion of the genomic nucleotide sequence forhuman B7-L polypeptide (SEQ ID NO: 15).

FIGS. 5A-5F illustrate a portion of the genomic nucleotide sequence forhuman B7-L polypeptide (SEQ ID NO: 16). The location of the deducedamino acid sequence of exon 2 (SEQ ID NO: 20) is indicated.

FIGS. 6A-6B illustrate a portion of the genomic nucleotide sequence forhuman B7-L polypeptide (SEQ ID NO: 17). The location of the deducedamino acid sequence of exon 3 (SEQ ID NO: 21) is indicated.

FIGS. 7A-7M illustrate a portion of the genomic nucleotide sequence forhuman B7-L polypeptide (SEQ ID NO: 18). The locations of the deducedamino acid sequence of exons 4 (SEQ ID NO: 22), 5 (SEQ ID NO: 23), and 6are indicated.

FIG. 8 shows the results for Northern blot analysis of human B7-L mRNAexpression.

FIG. 9 shows the results for fluorescence-activated cell sorter (FACS)analysis of CHO D-cells transfected with vector alone (A), or withvectors encoding PD-1 (B), CRP-1/ICOS (C) or CD28 (D), and incubatedwith either FITC alone, or with the following fusion proteins: CRP-1/Fc,B7-L polypeptide/Fc, B7rp-1/Fc, B7-H1/Fc, or B7-2/Fc.

FIG. 10 shows the results obtained in anti-CD3 mediated T-cellproliferation assays using B7-L polypeptide/Fc, B7RP-1/Fc, or B7-1/Fc.

FIG. 11 shows the results of FACS analysis of human peripheral bloodcells using FITC alone (A), Fc control (B), B7rp-1/Fc (C), B7-Lpolypeptide/Fc (D), B7-L polypeptide/Fc and anti-CD3 (E), or B7-Lpolypeptide/Fc and anti-CD19 (F).

DETAILED DESCRIPTION OF THE INVENTION

The section headings used herein are for organizational purposes onlyand are not to be construed as limiting the subject matter described.All references cited in this application are expressly incorporated byreference herein.

DEFINITIONS

The terms “B7-L gene” or “B7-L nucleic acid molecule” or “B7-Lpolynucleotide” refer to a nucleic acid molecule comprising orconsisting of a nucleotide sequence as set forth in SEQ ID NO: 1, anucleotide sequence encoding the polypeptide as set forth in SEQ ID NO:2, a nucleotide sequence of the DNA insert in ATCC Deposit No. PTA 2481,and nucleic acid molecules as defined herein.

The term “B7-L polypeptide allelic variant” refers to one of severalpossible naturally occurring alternate forms of a gene occupying a givenlocus on a chromosome of an organism or a population of organisms.

The term “137-L polypeptide splice variant” refers to a nucleic acidmolecule, usually RNA, which is generated by alternative processing ofintron sequences in an RNA transcript of B7-L polypeptide amino acidsequence as set forth in SEQ ID NO: 2.

The term “isolated nucleic acid molecule” refers to a nucleic acidmolecule of the invention that (1) has been separated from at leastabout 50 percent of proteins, lipids, carbohydrates, or other materialswith which it is naturally found when total nucleic acid is isolatedfrom the source cells, (2) is not linked to all or a portion of apolynucleotide to which the “isolated nucleic acid molecule” is linkedin nature, (3) is operably linked to a polynucleotide which it is notlinked to in nature, or (4) does not occur in nature as part of a largerpolynucleotide sequence. Preferably, the isolated nucleic acid moleculeof the present invention is substantially free from any othercontaminating nucleic acid molecule(s) or other contaminants that arefound in its natural environment that would interfere with its use inpolypeptide production or its therapeutic, diagnostic, prophylactic orresearch use.

The term “nucleic acid sequence” or “nucleic acid molecule” refers to aDNA or RNA sequence. The term encompasses molecules formed from any ofthe known base analogs of DNA and RNA such as, but not limited to4-acetylcytosine, 8-hydroxy-N6-methyladenosine, aziridinyl-cytosine,pseudoisocytosine, 5-(carboxyhydroxylmethyl) uracil, 5-fluorouracil,5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil,5-carboxy-methylaminomethyluracil, dihydrouracil, inosine,N6-iso-pentenyladenine, 1-methyladenine, 1-methylpseudouracil,1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine,2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-methyladenine,7-methylguanine, 5-methylaminomethyluracil,5-methoxyamino-methyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarbonyl-methyluracil, 5-methoxyuracil,2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methylester,uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine,2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil,5-methyluracil, N-uracil-5-oxyacetic acid methylester,uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and2,6-diaminopurine.

The term “vector” is used to refer to any molecule (e.g., nucleic acid,plasmid, or virus) used to transfer coding information to a host cell.

The term “expression vector” refers to a vector that is suitable fortransformation of a host cell and contains nucleic acid sequences thatdirect and/or control the expression of inserted heterologous nucleicacid sequences. Expression includes, but is not limited to, processessuch as transcription, translation, and RNA splicing, if introns arepresent.

The term “operably linked” is used herein to refer to an arrangement offlanking sequences wherein the flanking sequences so described areconfigured or assembled so as to perform their usual function. Thus, aflanking sequence operably linked to a coding sequence may be capable ofeffecting the replication, transcription and/or translation of thecoding sequence. For example, a coding sequence is operably linked to apromoter when the promoter is capable of directing transcription of thatcoding sequence. A flanking sequence need not be contiguous with thecoding sequence, so long as it functions correctly. Thus, for example,intervening untranslated yet transcribed sequences can be presentbetween a promoter sequence and the coding sequence and the promotersequence can still be considered “operably linked” to the codingsequence.

The term “host cell” is used to refer to a cell which has beentransformed, or is capable of being transformed with a nucleic acidsequence and then of expressing a selected gene of interest. The termincludes the progeny of the parent cell, whether or not the progeny isidentical in morphology or in genetic make-up to the original parent, solong as the selected gene is present.

The term “B7-L polypeptide” refers to a polypeptide comprising the aminoacid sequence of SEQ ID NO: 2 and related polypeptides. Relatedpolypeptides include B7-L polypeptide fragments, B7-L polypeptideorthologs, B7-L polypeptide variants, and B7-L polypeptide derivatives,which possess at least one activity of the polypeptide as set forth inSEQ ID NO: 2. B7-L polypeptides may be mature polypeptides, as definedherein, and may or may not have an amino-terminal methionine residue,depending on the method by which they are prepared.

The term “B7-L polypeptide fragment” refers to a polypeptide thatcomprises a truncation at the amino-terminus (with or without a leadersequence) and/or a truncation at the carboxyl-terminus of thepolypeptide as set forth in SEQ ID NO: 2. The term “B7-L polypeptidefragment” also refers to amino-terminal and/or carboxyl-terminaltruncations of B7-L polypeptide orthologs, B7-L polypeptide derivatives,or B 7-L polypeptide variants, or to amino-terminal and/orcarboxyl-terminal truncations of the polypeptides encoded by B7-Lpolypeptide allelic variants or B7-L polypeptide splice variants. B7-Lpolypeptide fragments may result from alternative RNA splicing or fromin vivo protease activity. Membrane-bound forms of a B7-L polypeptideare also contemplated by the present invention. In preferredembodiments, truncations and/or deletions comprise about 10 amino acids,or about 20 amino acids, or about 50 amino acids, or about 75 aminoacids, or about 100 amino acids, or more than about 100 amino acids. Thepolypeptide fragments so produced will comprise about 25 contiguousamino acids, or about 50 amino acids, or about 75 amino acids, or about100 amino acids, or about 150 amino acids, or about 200 amino acids.Such B7-L polypeptide fragments may optionally comprise anamino-terminal methionine residue. It will be appreciated that suchfragments can be used, for example, to generate antibodies to B7-Lpolypeptides.

The term “B7-L polypeptide ortholog” refers to a polypeptide fromanother species that corresponds to B7-L polypeptide amino acid sequenceas set forth in SEQ ID NO: 2. For example, mouse and human B7-Lpolypeptides are considered orthologs of each other.

The term “B7-L polypeptide variants” refers to B7-L polypeptidescomprising amino acid sequences having one or more amino acid sequencesubstitutions, deletions (such as internal deletions and/or B7-Lpolypeptide fragments), and/or additions (such as internal additionsand/or B7-L fusion polypeptides) as compared to the B7-L polypeptideamino acid sequence set forth in SEQ ID NO: 2 (with or without a leadersequence). Variants may be naturally occurring (e.g., B7-L polypeptideallelic variants, B7-L polypeptide orthologs, and B7-L polypeptidesplice variants) or artificially constructed. Such B7-L polypeptidevariants may be prepared from the corresponding nucleic acid moleculeshaving a DNA sequence that varies accordingly from the DNA sequence asset forth in SEQ ID NO: 1. In preferred embodiments, the variants havefrom 1 to 3, or from 1 to 5, or from 1 to 10, or from 1 to 15, or from 1to 20, or from 1 to 25, or from 1 to 50, or from 1 to 75, or from 1 to100, or more than 100 amino acid substitutions, insertions, additionsand/or deletions, wherein the substitutions may be conservative, ornon-conservative, or any combination thereof.

The term “B7-L polypeptide derivatives” refers to the polypeptide as setforth in SEQ ID NO: 2, B7-L polypeptide fragments, B7-L polypeptideorthologs, or B7-L polypeptide variants, as defined herein, that havebeen chemically modified. The term “B7-L polypeptide derivatives” alsorefers to the polypeptides encoded by B7-L polypeptide allelic variantsor B7-L polypeptide splice variants, as defined herein, that have beenchemically modified.

The term “mature B7-L polypeptide” refers to a B7-L polypeptide lackinga leader sequence. A mature B7-L polypeptide may also include othermodifications such as proteolytic processing of the amino-terminus (withor without a leader sequence) and/or the carboxyl-terminus, cleavage ofa smaller polypeptide from a larger precursor, N-linked and/or O-linkedglycosylation, and the like. An exemplary mature B7-L polypeptide isdepicted by the amino acid sequence of SEQ ID NO: 3.

The term “B7-L fusion polypeptide” refers to a fusion of one or moreamino acids (such as a heterologous protein or peptide) at the amino- orcarboxyl-terminus of the polypeptide as set forth in SEQ ID NO: 2, B 7-Lpolypeptide fragments, B7-L polypeptide orthologs, B7-L polypeptidevariants, or B7-L derivatives, as defined herein. The term “B7-L fusionpolypeptide” also refers to a fusion of one or more amino acids at theamino- or carboxyl-terminus of the polypeptide encoded by B7-Lpolypeptide allelic variants or B7-L polypeptide splice variants, asdefined herein.

The term “biologically active B7-L polypeptides” refers to B7-Lpolypeptides having at least one activity characteristic of thepolypeptide comprising the amino acid sequence of SEQ ID NO: 2. Inaddition, a B7-L polypeptide may be active as an immunogen; that is, theB7-L polypeptide contains at least one epitope to which antibodies maybe raised.

The term “isolated polypeptide” refers to a polypeptide of the presentinvention that (1) has been separated from at least about 50 percent ofpolynucleotides, lipids, carbohydrates, or other materials with which itis naturally found when isolated from the source cell, (2) is not linked(by covalent or noncovalent interaction) to all or a portion of apolypeptide to which the “isolated polypeptide” is linked in nature, (3)is operably linked (by covalent or noncovalent interaction) to apolypeptide with which it is not linked in nature, or (4) does not occurin nature. Preferably, the isolated polypeptide is substantially freefrom any other contaminating polypeptides or other contaminants that arefound in its natural environment that would interfere with itstherapeutic, diagnostic, prophylactic or research use.

The term “identity,” as known in the art, refers to a relationshipbetween the sequences of two or more polypeptide molecules or two ormore nucleic acid molecules, as determined by comparing the sequences.In the art, “identity” also means the degree of sequence relatednessbetween nucleic acid molecules or polypeptides, as the case may be, asdetermined by the match between strings of two or more nucleotide or twoor more amino acid sequences. “Identity” measures the percent ofidentical matches between the smaller of two or more sequences with gapalignments (if any) addressed by a particular mathematical model orcomputer program (i.e., “algorithms”).

The term “similarity” is a related concept, but in contrast to“identity,” “similarity” refers to a measure of relatedness thatincludes both identical matches and conservative substitution matches.If two polypeptide sequences have, for example, 10/20 identical aminoacids, and the remainder are all non-conservative substitutions, thenthe percent identity and similarity would both be 50%. If in the sameexample, there are five more positions where there are conservativesubstitutions, then the percent identity remains 50%, but the percentsimilarity would be 75% ( 15/20). Therefore, in cases where there areconservative substitutions, the percent similarity between twopolypeptides will be higher than the percent identity between those twopolypeptides.

The term “naturally occurring” or “native” when used in connection withbiological materials such as nucleic acid molecules, polypeptides, hostcells, and the like, refers to materials which are found in nature andare not manipulated by man. Similarly, “non-naturally occurring” or“non-native” as used herein refers to a material that is not found innature or that has been structurally modified or synthesized by man.

The terms “effective amount” and “therapeutically effective amount” eachrefer to the amount of a B7-L polypeptide or B7-L nucleic acid moleculeused to support an observable level of one or more biological activitiesof the B7-L polypeptides as set forth herein.

The term “pharmaceutically acceptable carrier” or “physiologicallyacceptable carrier” as used herein refers to one or more formulationmaterials suitable for accomplishing or enhancing the delivery of theB7-L polypeptide, B7-L nucleic acid molecule, or B7-L selective bindingagent as a pharmaceutical composition.

The term “antigen” refers to a molecule or a portion of a moleculecapable of being bound by a selective binding agent, such as anantibody, and additionally capable of being used in an animal to produceantibodies capable of binding to an epitope of that antigen. An antigenmay have one or more epitopes.

The term “selective binding agent” refers to a molecule or moleculeshaving specificity for a B7-L polypeptide. As used herein, the terms,“specific” and “specificity” refer to the ability of the selectivebinding agents to bind to human B7-L polypeptides and not to bind tohuman non-B7-L polypeptides. It will be appreciated, however, that theselective binding agents may also bind orthologs of the polypeptide asset forth in SEQ ID NO: 2, that is, interspecies versions thereof, suchas mouse and rat B7-L polypeptides.

The term “transduction” is used to refer to the transfer of genes fromone bacterium to another, usually by a phage. “Transduction” also refersto the acquisition and transfer of eukaryotic cellular sequences byretroviruses.

The term “transfection” is used to refer to the uptake of foreign orexogenous DNA by a cell, and a cell has been “transfected” when theexogenous DNA has been introduced inside the cell membrane. A number oftransfection techniques are well known in the art and are disclosedherein. See, e.g., Graham et al., 1973, Virology 52:456; Sambrook etal., Molecular Cloning, A Laboratory Manual (Cold Spring HarborLaboratories, 1989); Davis et al., Basic Methods in Molecular Biology(Elsevier, 1986); and Chu et al., 1981, Gene 13:197. Such techniques canbe used to introduce one or more exogenous DNA moieties into suitablehost cells.

The term “transformation” as used herein refers to a change in a cell'sgenetic characteristics, and a cell has been transformed when it hasbeen modified to contain a new DNA. For example, a cell is transformedwhere it is genetically modified from its native state. Followingtransfection or transduction, the transforming DNA may recombine withthat of the cell by physically integrating into a chromosome of thecell, may be maintained transiently as an episomal element without beingreplicated, or may replicate independently as a plasmid. A cell isconsidered to have been stably transformed when the DNA is replicatedwith the division of the cell.

Relatedness of Nucleic Acid Molecules and/or Polypeptides

It is understood that related nucleic acid molecules include allelic orsplice variants of the nucleic acid molecule of SEQ ID NO: 1, andinclude sequences which are complementary to any of the above nucleotidesequences. Related nucleic acid molecules also include a nucleotidesequence encoding a polypeptide comprising or consisting essentially ofa substitution, modification, addition and/or deletion of one or moreamino acid residues compared to the polypeptide as set forth in SEQ IDNO: 2. Such related B7-L-polypeptides may comprise, for example, anaddition and/or a deletion of one or more N-linked or O-linkedglycosylation sites or an addition and/or a deletion of one or morecysteine residues.

Related nucleic acid molecules also include fragments of B7-L nucleicacid molecules which encode a polypeptide of at least about 25contiguous amino acids, or about 50 amino acids, or about 75 aminoacids, or about 100 amino acids, or about 150 amino acids, or about 200amino acids, or more than 200 amino acid residues of the B7-Lpolypeptide of SEQ ID NO: 2.

In addition, related B7-L nucleic acid molecules also include thosemolecules which comprise nucleotide sequences which hybridize undermoderately or highly stringent conditions as defined herein with thefully complementary sequence of the B7-L nucleic acid molecule of SEQ IDNO: 1, or of a molecule encoding a polypeptide, which polypeptidecomprises the amino acid sequence as shown in SEQ ID NO: 2, or of anucleic acid fragment as defined herein, or of a nucleic acid fragmentencoding a polypeptide as defined herein. Hybridization probes may beprepared using the B7-L sequences provided herein to screen cDNA,genomic or synthetic DNA libraries for related sequences. Regions of theDNA and/or amino acid sequence of B7-L polypeptide that exhibitsignificant identity to known sequences are readily determined usingsequence alignment algorithms as described herein and those regions maybe used to design probes for screening.

The term “highly stringent conditions” refers to those conditions thatare designed to permit hybridization of DNA strands whose sequences arehighly complementary, and to exclude hybridization of significantlymismatched DNAs. Hybridization stringency is principally determined bytemperature, ionic strength, and the concentration of denaturing agentssuch as formamide. Examples of “highly stringent conditions” forhybridization and washing are 0.015 M sodium chloride, 0.0015 M sodiumcitrate at 65-68° C. or 0.015 M sodium chloride, 0.0015 M sodiumcitrate, and 50% formamide at 42° C. See Sambrook, Fritsch & Maniatis,Molecular Cloning: A Laboratory Manual (2nd ed., Cold Spring HarborLaboratory, 1989); Anderson et al., Nucleic Acid Hybridisation: APractical Approach Ch. 4 (IRL Press Limited).

More stringent conditions (such as higher temperature, lower ionicstrength, higher formamide, or other denaturing agent) may also beused—however, the rate of hybridization will be affected. Other agentsmay be included in the hybridization and washing buffers for the purposeof reducing non-specific and/or background hybridization. Examples are0.1% bovine serum albumin, 0.1% polyvinyl-pyrrolidone, 0.1% sodiumpyrophosphate, 0.1% sodium dodecylsulfate, NaDodSO₄, (SDS), ficoll,Denhardt's solution, sonicated salmon sperm DNA (or anothernon-complementary DNA), and dextran sulfate, although other suitableagents can also be used. The concentration and types of these additivescan be changed without substantially affecting the stringency of thehybridization conditions. Hybridization experiments are usually carriedout at pH 6.8-7.4; however, at typical ionic strength conditions, therate of hybridization is nearly independent of pH. See Anderson et al.,Nucleic Acid Hybridisation: A Practical Approach Ch. 4 (IRL PressLimited).

Factors affecting the stability of DNA duplex include base composition,length, and degree of base pair mismatch. Hybridization conditions canbe adjusted by one skilled in the art in order to accommodate thesevariables and allow DNAs of different sequence relatedness to formhybrids. The melting temperature of a perfectly matched DNA duplex canbe estimated by the following equation:

T_(m)(° C.)=81.5+16.6(log [Na+])+0.41(%G+C)−600/N−0.72(% formamide)

where N is the length of the duplex formed, [Na+] is the molarconcentration of the sodium ion in the hybridization or washingsolution, % G+C is the percentage of (guanine+cytosine) bases in thehybrid. For imperfectly matched hybrids, the melting temperature isreduced by approximately 1° C. for each 1% mismatch.

The term “moderately stringent conditions” refers to conditions underwhich a DNA duplex with a greater degree of base pair mismatching thancould occur under “highly stringent conditions” is able to form.Examples of typical “moderately stringent conditions” are 0.015 M sodiumchloride, 0.0015 M sodium citrate at 50-65° C. or 0.015 M sodiumchloride, 0.0015 M sodium citrate, and 20% formamide at 37-50° C. By wayof example, “moderately stringent conditions” of 50° C. in 0.015 Msodium ion will allow about a 21% mismatch.

It will be appreciated by those skilled in the art that there is noabsolute distinction between “highly stringent conditions” and“moderately stringent conditions.” For example, at 0.015 M sodium ion(no formamide), the melting temperature of perfectly matched long DNA isabout 71° C. With a wash at 65° C. (at the same ionic strength), thiswould allow for approximately a 6% mismatch. To capture more distantlyrelated sequences, one skilled in the art can simply lower thetemperature or raise the ionic strength.

A good estimate of the melting temperature in 1M NaCl* foroligonucleotide probes up to about 20 nt is given by:

Tm=2° C. per A-T base pair+4° C. per G-C base pair

*The sodium ion concentration in 6× salt sodium citrate (SSC) is 1M. SeeSuggs et al., Developmental Biology Using Purified Genes 683 (Brown andFox, eds., 1981).

High stringency washing conditions for oligonucleotides are usually at atemperature of 0-5° C. below the Tm of the oligonucleotide in 6×SSC,0.1% SDS.

In another embodiment, related nucleic acid molecules comprise orconsist of a nucleotide sequence that is at least about 70 percentidentical to the nucleotide sequence as shown in SEQ ID NO: 1. Inpreferred embodiments, the nucleotide sequences are about 75 percent, orabout 80 percent, or about 85 percent, or about 90 percent, or about 95,96, 97, 98, or 99 percent identical to the nucleotide sequence as shownin SEQ ID NO: 1. Related nucleic acid molecules encode polypeptidespossessing at least one activity of the polypeptide set forth in SEQ IDNO: 2.

Differences in the nucleic acid sequence may result in conservativeand/or non-conservative modifications of the amino acid sequencerelative to the amino acid sequence of SEQ ID NO: 2.

Conservative modifications to the amino acid sequence of SEQ ID NO: 2(and the corresponding modifications to the encoding nucleotides) willproduce a polypeptide having functional and chemical characteristicssimilar to those of B7-L polypeptides. In contrast, substantialmodifications in the functional and/or chemical characteristics of B7-Lpolypeptides may be accomplished by selecting substitutions in the aminoacid sequence of SEQ ID NO: 2 that differ significantly in their effecton maintaining (a) the structure of the molecular backbone in the areaof the substitution, for example, as a sheet or helical conformation,(b) the charge or hydrophobicity of the molecule at the target site, or(c) the bulk of the side chain.

For example, a “conservative amino acid substitution” may involve asubstitution of a native amino acid residue with a normative residuesuch that there is little or no effect on the polarity or charge of theamino acid residue at that position. Furthermore, any native residue inthe polypeptide may also be substituted with alanine, as has beenpreviously described for “alanine scanning mutagenesis.”

Conservative amino acid substitutions also encompass non-naturallyoccurring amino acid residues that are typically incorporated bychemical peptide synthesis rather than by synthesis in biologicalsystems. These include peptidomimetics, and other reversed or invertedforms of amino acid moieties.

Naturally occurring residues may be divided into classes based on commonside chain properties:

1) hydrophobic: norleucine, Met, Ala, Val, Leu, Ile;

2) neutral hydrophilic: Cys, Ser, Thr;

3) acidic: Asp, Glu;

4) basic: Asn, Gln, His, Lys, Arg;

5) residues that influence chain orientation: Gly, Pro; and

6) aromatic: Trp, Tyr, Phe.

For example, non-conservative substitutions may involve the exchange ofa member of one of these classes for a member from another class. Suchsubstituted residues may be introduced into regions of the human B7-Lpolypeptide that are homologous with non-human B7-L polypeptides, orinto the non-homologous regions of the molecule.

In making such changes, the hydropathic index of amino acids may beconsidered. Each amino acid has been assigned a hydropathic index on thebasis of its hydrophobicity and charge characteristics. The hydropathicindices are: isoleucine (+4.5); valine (+4.2); leucine (+3.8);phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9);alamine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8);tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2);glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5);lysine (−3.9); and arginine (−4.5).

The importance of the hydropathic amino acid index in conferringinteractive biological function on a protein is generally understood inthe art (Kyte et al., 1982, J. Mol. Biol. 157:105-31). It is known thatcertain amino acids may be substituted for other amino acids having asimilar hydropathic index or score and still retain a similar biologicalactivity. In making changes based upon the hydropathic index, thesubstitution of amino acids whose hydropathic indices are within ±2 ispreferred, those that are within ±1 are particularly preferred, andthose within ±0.5 are even more particularly preferred.

It is also understood in the art that the substitution of like aminoacids can be made effectively on the basis of hydrophilicity,particularly where the biologically functionally equivalent protein orpeptide thereby created is intended for use in immunologicalembodiments, as in the present case. The greatest local averagehydrophilicity of a protein, as governed by the hydrophilicity of itsadjacent amino acids, correlates with its immunogenicity andantigenicity, i.e., with a biological property of the protein.

The following hydrophilicity values have been assigned to these aminoacid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1);glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2);glycine (0); threonine (−0.4); proline (−0.5±1); alanine (−0.5);histidine (−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5);leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine(−2.5); and tryptophan (−3.4). In making changes based upon similarhydrophilicity values, the substitution of amino acids whosehydrophilicity values are within ±2 is preferred, those that are within±1 are particularly preferred, and those within ±0.5 are even moreparticularly preferred. One may also identify epitopes from primaryamino acid sequences on the basis of hydrophilicity. These regions arealso referred to as “epitopic core regions.”

Desired amino acid substitutions (whether conservative ornon-conservative) can be determined by those skilled in the art at thetime such substitutions are desired. For example, amino acidsubstitutions can be used to identify important residues of the B7-Lpolypeptide, or to increase or decrease the affinity of the B7-Lpolypeptides described herein. Exemplary amino acid substitutions areset forth in Table I.

TABLE I Amino Acid Substitutions Original Residues ExemplarySubstitutions Preferred Substitutions Ala Val, Leu, Ile Val Arg Lys,Gln, Asn Lys Asn Gln Gln Asp Glu Glu Cys Ser, Ala Ser Gln Asn Asn GluAsp Asp Gly Pro, Ala Ala His Asn, Gln, Lys, Arg Arg Ile Leu, Val, Met,Ala, Leu Phe, Norleucine Leu Norleucine, Ile, Ile Val, Met, Ala, Phe LysArg, 1,4 Diamino-butyric Arg Acid, Gln, Asn Met Leu, Phe, Ile Leu PheLeu, Val, Ile, Ala, Leu Tyr Pro Ala Gly Ser Thr, Ala, Cys Thr Thr SerSer Trp Tyr, Phe Tyr Tyr Trp, Phe, Thr, Ser Phe Val Ile, Met, Leu, Phe,Leu Ala, Norleucine

A skilled artisan will be able to determine suitable variants of thepolypeptide as set forth in SEQ ID NO: 2 using well-known techniques.For identifying suitable areas of the molecule that may be changedwithout destroying biological activity, one skilled in the art maytarget areas not believed to be important for activity. For example,when similar polypeptides with similar activities from the same speciesor from other species are known, one skilled in the art may compare theamino acid sequence of a B7-L polypeptide to such similar polypeptides.With such a comparison, one can identify residues and portions of themolecules that are conserved among similar polypeptides. It will beappreciated that changes in areas of the B7-L molecule that are notconserved relative to such similar polypeptides would be less likely toadversely affect the biological activity and/or structure of a B7-Lpolypeptide. One skilled in the art would also know that, even inrelatively conserved regions, one may substitute chemically similaramino acids for the naturally occurring residues while retainingactivity (conservative amino acid residue substitutions). Therefore,even areas that may be important for biological activity or forstructure may be subject to conservative amino acid substitutionswithout destroying the biological activity or without adverselyaffecting the polypeptide structure.

Additionally, one skilled in the art can review structure-functionstudies identifying residues in similar polypeptides that are importantfor activity or structure. In view of such a comparison, one can predictthe importance of amino acid residues in a B7-L polypeptide thatcorrespond to amino acid residues that are important for activity orstructure in similar polypeptides. One skilled in the art may opt forchemically similar amino acid substitutions for such predicted importantamino acid residues of B7-L polypeptides.

One skilled in the art can also analyze the three-dimensional structureand amino acid sequence in relation to that structure in similarpolypeptides. In view of such information, one skilled in the art maypredict the alignment of amino acid residues of B7-L polypeptide withrespect to its three dimensional structure. One skilled in the art maychoose not to make radical changes to amino acid residues predicted tobe on the surface of the protein, since such residues may be involved inimportant interactions with other molecules. Moreover, one skilled inthe art may generate test variants containing a single amino acidsubstitution at each amino acid residue. The variants could be screenedusing activity assays known to those with skill in the art. Suchvariants could be used to gather information about suitable variants.For example, if one discovered that a change to a particular amino acidresidue resulted in destroyed, undesirably reduced, or unsuitableactivity, variants with such a change would be avoided. In other words,based on information gathered from such routine experiments, one skilledin the art can readily determine the amino acids where furthersubstitutions should be avoided either alone or in combination withother mutations.

A number of scientific publications have been devoted to the predictionof secondary structure. See Moult, 1996, Curr. Opin. Biotechnol.7:422-27; Chou et al., 1974, Biochemistry 13:222-45; Chou et al., 1974,Biochemistry 113:211-22; Chou et al., 1978, Adv. Enzymol. Relat. AreasMol. Biol. 47:45-48; Chou et al., 1978, Ann. Rev. Biochem. 47:251-276;and Chou et al., 1979, Biophys. J. 26:367-84. Moreover, computerprograms are currently available to assist with predicting secondarystructure. One method of predicting secondary structure is based uponhomology modeling. For example, two polypeptides or proteins that have asequence identity of greater than 30%, or similarity greater than 40%,often have similar structural topologies. The recent growth of theprotein structural database (PDB) has provided enhanced predictabilityof secondary structure, including the potential number of folds withinthe structure of a polypeptide or protein. See Holm et al., 1999,Nucleic Acids Res. 27:244-47. It has been suggested that there are alimited number of folds in a given polypeptide or protein and that oncea critical number of structures have been resolved, structuralprediction will become dramatically more accurate (Brenner et al., 1997,Curr. Opin. Struct. Biol. 7:369-76).

Additional methods of predicting secondary structure include “threading”(Jones, 1997, Curr. Opin. Struct. Biol. 7:377-87; Sippl et al., 1996,Structure 4:15-19), “profile analysis” (Bowie et al., 1991, Science,253:164-70; Gribskov et al., 1990, Methods Enzymol. 183:146-59; Gribskovet al., 1987, Proc. Nat. Acad. Sci. U.S.A. 84:4355-58), and“evolutionary linkage” (See Holm et al., supra, and Brenner et al.,supra).

Preferred B7-L polypeptide variants include glycosylation variantswherein the number and/or type of glycosylation sites have been alteredcompared to the amino acid sequence set forth in SEQ ID NO: 2. In oneembodiment, B7-L polypeptide variants comprise a greater or a lessernumber of N-linked glycosylation sites than the amino acid sequence setforth in SEQ ID NO: 2. An N-linked glycosylation site is characterizedby the sequence: Asn-X-Ser or Asn-X-Thr, wherein the amino acid residuedesignated as X may be any amino acid residue except proline. Thesubstitution of amino acid residues to create this sequence provides apotential new site for the addition of an N-linked carbohydrate chain.Alternatively, substitutions that eliminate this sequence will remove anexisting N-linked carbohydrate chain. Also provided is a rearrangementof N-linked carbohydrate chains wherein one or more N-linkedglycosylation sites (typically those that are naturally occurring) areeliminated and one or more new N-linked sites are created. Additionalpreferred B7-L variants include cysteine variants, wherein one or morecysteine residues are deleted or substituted with another amino acid(e.g. serine) as compared to the amino acid sequence set forth in SEQ IDNO: 2. Cysteine variants are useful when B7-L polypeptides must berefolded into a biologically active conformation such as after theisolation of insoluble inclusion bodies. Cysteine variants generallyhave fewer cysteine residues than the native protein, and typically havean even number to minimize interactions resulting from unpairedcysteines.

In other embodiments, B7-L polypeptide variants comprise an amino acidsequence as set forth in SEQ ID NO: 2 with at least one amino acidinsertion and wherein the polypeptide has an activity of the polypeptideset forth in SEQ ID NO: 2, or an amino acid sequence as set forth in SEQID NO: 2 with at least one amino acid deletion and wherein thepolypeptide has an activity of the polypeptide set forth in SEQ ID NO:2. B7-L polypeptide variants also comprise an amino acid sequence as setforth in SEQ ID NO: 2 wherein the polypeptide has a carboxyl- and/oramino-terminal truncation and further wherein the polypeptide has anactivity of the polypeptide set forth in SEQ ID NO: 2. B7-L polypeptidevariants further comprise an amino acid sequence as set forth in SEQ IDNO: 2 with at least one modification selected from the group consistingof amino acid substitutions, amino acid insertions, amino aciddeletions, carboxyl-terminal truncations, and amino-terminal truncationsand wherein the polypeptide has an activity of the polypeptide set forthin SEQ ID NO: 2.

In further embodiments, B7-L polypeptide variants comprise an amino acidsequence that is at least about 70 percent identical to the amino acidsequence as set forth in SEQ ID NO: 2. In preferred embodiments, B7-Lpolypeptide variants comprise an amino acid sequence that is about 75percent, or about 80 percent, or about 85 percent, or about 90 percent,or about 95, 96, 97, 98, or 99 percent identical to the amino acidsequence as set forth in SEQ ID NO: 2. B7-L polypeptide variants possessat least one activity of the polypeptide set forth in SEQ ID NO: 2.

In addition, the polypeptide comprising the amino acid sequence of SEQID NO: 2, or other B7-L polypeptide, may be fused to a homologouspolypeptide to form a homodimer or to a heterologous polypeptide to forma heterodimer. Heterologous peptides and polypeptides include, but arenot limited to: an epitope to allow for the detection and/or isolationof a B7-L fusion polypeptide; a transmembrane receptor protein or aportion thereof, such as an extracellular domain or a transmembrane andintracellular domain; a ligand or a portion thereof which binds to atransmembrane receptor protein; an enzyme or portion thereof which iscatalytically active; a polypeptide or peptide which promotesoligomerization, such as a leucine zipper domain; a polypeptide orpeptide which increases stability, such as an immunoglobulin constantregion; and a polypeptide which has a therapeutic activity differentfrom the polypeptide comprising the amino acid sequence as set forth inSEQ ID NO: 2, or other B7-L polypeptide.

Fusions can be made either at the amino-terminus or at thecarboxyl-terminus of the polypeptide comprising the amino acid sequenceset forth in SEQ ID NO: 2, or other B7-L polypeptide. Fusions may bedirect with no linker or adapter molecule or may be through a linker oradapter molecule. A linker or adapter molecule may be one or more aminoacid residues, typically from about 20 to about 50 amino acid residues.A linker or adapter molecule may also be designed with a cleavage sitefor a DNA restriction endonuclease or for a protease to allow for theseparation of the fused moieties. It will be appreciated that onceconstructed, the fusion polypeptides can be derivatized according to themethods described herein.

In a further embodiment of the invention, the polypeptide comprising theamino acid sequence of SEQ ID NO: 2, or other B7-L polypeptide, is fusedto one or more domains of an Fc region of human IgG. Antibodies comprisetwo functionally independent parts, a variable domain known as “Fab,”that binds an antigen, and a constant domain known as “Fc,” that isinvolved in effector functions such as complement activation and attackby phagocytic cells. An Fc has a long serum half-life, whereas an Fab isshort-lived. Capon et al., 1989, Nature 337:525-31. When constructedtogether with a therapeutic protein, an Fc domain can provide longerhalf-life or incorporate such functions as Fc receptor binding, proteinA binding, complement fixation, and perhaps even placental transfer. Id.Table II summarizes the use of certain Fc fusions known in the art.

TABLE II Fc Fusion with Therapeutic Proteins Form of Fc Fusion partnerTherapeutic implications Reference IgG1 N-terminus of Hodgkin's disease;U.S. Pat. No. CD30-L anaplastic lymphoma; T- 5,480,981 cell leukemiaMurine Fcγ2a IL-10 anti-inflammatory; Zheng et al., 1995, J. transplantrejection Immunol. 154: 5590-600 IgG1 TNF receptor septic shock Fisheret al., 1996, N. Engl. J. Med. 334: 1697- 1702; Van Zee et al., 1996, J.Immunol. 156: 2221-30 IgG, IgA, IgM, TNF receptor inflammation, U.S.Pat. No. or IgE autoimmune disorders 5,808,029 (excluding the firstdomain) IgG1 CD4 receptor AIDS Capon et al., 1989, Nature 337: 525-31IgG1, IgG3 N-terminus anti-cancer, antiviral Harvill et al., 1995, ofIL-2 Immunotech. 1: 95-105 IgG1 C-terminus of osteoarthritis; WO97/23614 OPG bone density IgG1 N-terminus of anti-obesity PCT/US97/23183, filed leptin Dec. 11, 1997 Human Ig Cγ1 CTLA-4 autoimmunedisorders Linsley, 1991, J. Exp. Med., 174: 561-69

In one example, a human IgG hinge, CH2, and CH3 region may be fused ateither the amino-terminus or carboxyl-terminus of the B7-L polypeptidesusing methods known to the skilled artisan. In another example, a humanIgG hinge, CH2, and CH3 region may be fused at either the amino-terminusor carboxyl-terminus of a B7-L polypeptide fragment (e.g., the predictedextracellular portion of B7-L polypeptide).

The resulting B7-L fusion polypeptide may be purified by use of aProtein A affinity column. Peptides and proteins fused to an Fc regionhave been found to exhibit a substantially greater half-life in vivothan the unfused counterpart. Also, a fusion to an Fc region allows fordimerization/multimerization of the fusion polypeptide. The Fc regionmay be a naturally occurring Fc region, or may be altered to improvecertain qualities, such as therapeutic qualities, circulation time, orreduced aggregation.

Identity and similarity of related nucleic acid molecules andpolypeptides are readily calculated by known methods. Such methodsinclude, but are not limited to those described in ComputationalMolecular Biology (A. M. Lesk, ed., Oxford University Press 1988);Biocomputing: Informatics and Genome Projects (D. W. Smith, ed.,Academic Press 1993); Computer Analysis of Sequence Data (Part 1, A. M.Griffin and H. G. Griffin, eds., Humana Press 1994); G. von Heinle,Sequence Analysis in Molecular Biology (Academic Press 1987); SequenceAnalysis Primer (M. Gribskov and J. Devereux, eds., M. Stockton Press1991); and Carillo et al., 1988, SIAM J. Applied Math., 48:1073.

Preferred methods to determine identity and/or similarity are designedto give the largest match between the sequences tested. Methods todetermine identity and similarity are described in publicly availablecomputer programs. Preferred computer program methods to determineidentity and similarity between two sequences include, but are notlimited to, the GCG program package, including GAP (Devereux et al.,1984, Nucleic Acids Res. 12:387; Genetics Computer Group, University ofWisconsin, Madison, Wis.), BLASTP, BLASTN, and FASTA (Altschul et al.,1990, J. Mol. Biol. 215:403-10). The BLASTX program is publiclyavailable from the National Center for Biotechnology Information (NCBI)and other sources (Altschul et al., BLAST Manual NCB NLM NIH, Bethesda,Md.); Altschul et al., 1990, supra). The well-known Smith Watermanalgorithm may also be used to determine identity.

Certain alignment schemes for aligning two amino acid sequences mayresult in the matching of only a short region of the two sequences, andthis small aligned region may have very high sequence identity eventhough there is no significant relationship between the two full-lengthsequences. Accordingly, in a preferred embodiment, the selectedalignment method (GAP program) will result in an alignment that spans atleast 50 contiguous amino acids of the claimed polypeptide.

For example, using the computer algorithm GAP (Genetics Computer Group,University of Wisconsin, Madison, Wis.), two polypeptides for which thepercent sequence identity is to be determined are aligned for optimalmatching of their respective amino acids (the “matched span,” asdetermined by the algorithm). A gap opening penalty (which is calculatedas 3× the average diagonal; the “average diagonal” is the average of thediagonal of the comparison matrix being used; the “diagonal” is thescore or number assigned to each perfect amino acid match by theparticular comparison matrix) and a gap extension penalty (which isusually 0.1× the gap opening penalty), as well as a comparison matrixsuch as PAM 250 or BLOSUM 62 are used in conjunction with the algorithm.A standard comparison matrix is also used by the algorithm (see Dayhoffet al., 5 Atlas of Protein Sequence and Structure (Supp. 3 1978) (PAM250comparison matrix); Henikoff et al., 1992, Proc. Natl. Acad. Sci. USA89:10915-19 (BLOSUM 62 comparison matrix)).

Preferred parameters for polypeptide sequence comparison include thefollowing:

Algorithm: Needleman and Wunsch, 1970, J. Mol. Biol. 48:443-53;

Comparison matrix: BLOSUM 62 (Henikoff et al., supra);

Gap Penalty: 12

Gap Length Penalty: 4

Threshold of Similarity: 0

The GAP program is useful with the above parameters. The aforementionedparameters are the default parameters for polypeptide comparisons (alongwith no penalty for end gaps) using the GAP algorithm.

Preferred parameters for nucleic acid molecule sequence comparisoninclude the following:

Algorithm: Needleman and Wunsch, supra;

Comparison matrix: matches=+10, mismatch=0

Gap Penalty: 50

Gap Length Penalty: 3

The GAP program is also useful with the above parameters. Theaforementioned parameters are the default parameters for nucleic acidmolecule comparisons.

Other exemplary algorithms, gap opening penalties, gap extensionpenalties, comparison matrices, and thresholds of similarity may beused, including those set forth in the Program Manual, WisconsinPackage, Version 9, September, 1997. The particular choices to be madewill be apparent to those of skill in the art and will depend on thespecific comparison to be made, such as DNA-to-DNA, protein-to-protein,protein-to-DNA; and additionally, whether the comparison is betweengiven pairs of sequences (in which case GAP or BestFit are generallypreferred) or between one sequence and a large database of sequences (inwhich case FASTA or BLASTA are preferred).

Nucleic Acid Molecules

The nucleic acid molecules encoding a polypeptide comprising the aminoacid sequence of a B7-L polypeptide can readily be obtained in a varietyof ways including, without limitation, chemical synthesis, cDNA orgenomic library screening, expression library screening, and/or PCRamplification of cDNA.

Recombinant DNA methods used herein are generally those set forth inSambrook et al., Molecular Cloning: A Laboratory Manual (Cold SpringHarbor Laboratory Press, 1989) and/or Current Protocols in MolecularBiology (Ausubel et al., eds., Green Publishers Inc. and Wiley and Sons1994). The invention provides for nucleic acid molecules as describedherein and methods for obtaining such molecules.

Where a gene encoding the amino acid sequence of a B7-L polypeptide hasbeen identified from one species, all or a portion of that gene may beused as a probe to identify orthologs or related genes from the samespecies. The probes or primers may be used to screen cDNA libraries fromvarious tissue sources believed to express the B7-L polypeptide. Inaddition, part or all of a nucleic acid molecule having the sequence asset forth in SEQ ID NO: 1 may be used to screen a genomic library toidentify and isolate a gene encoding the amino acid sequence of a B7-Lpolypeptide. Typically, conditions of moderate or high stringency willbe employed for screening to minimize the number of false positivesobtained from the screening.

Nucleic acid molecules encoding the amino acid sequence of B7-Lpolypeptides may also be identified by expression cloning which employsthe detection of positive clones based upon a property of the expressedprotein. Typically, nucleic acid libraries are screened by the bindingan antibody or other binding partner (e.g., receptor or ligand) tocloned proteins that are expressed and displayed on a host cell surface.The antibody or binding partner is modified with a detectable label toidentify those cells expressing the desired clone.

Recombinant expression techniques conducted in accordance with thedescriptions set forth below may be followed to produce thesepolynucleotides and to express the encoded polypeptides. For example, byinserting a nucleic acid sequence that encodes the amino acid sequenceof a B7-L polypeptide into an appropriate vector, one skilled in the artcan readily produce large quantities of the desired nucleotide sequence.The sequences can then be used to generate detection probes oramplification primers. Alternatively, a polynucleotide encoding theamino acid sequence of a B7-L polypeptide can be inserted into anexpression vector. By introducing the expression vector into anappropriate host, the encoded B7-L polypeptide may be produced in largeamounts.

Another method for obtaining a suitable nucleic acid sequence is thepolymerase chain reaction (PCR). In this method, cDNA is prepared frompoly(A)+ RNA or total RNA using the enzyme reverse transcriptase. Twoprimers, typically complementary to two separate regions of cDNAencoding the amino acid sequence of a B7-L polypeptide, are then addedto the cDNA along with a polymerase such as Taq polymerase, and thepolymerase amplifies the cDNA region between the two primers.

Another means of preparing a nucleic acid molecule encoding the aminoacid sequence of a B7-L polypeptide is chemical synthesis using methodswell known to the skilled artisan such as those described by Engels etal., 1989, Angew. Chem. Intl. Ed. 28:716-34. These methods include,inter alia, the phosphotriester, phosphoramidite, and H-phosphonatemethods for nucleic acid synthesis. A preferred method for such chemicalsynthesis is polymer-supported synthesis using standard phosphoramiditechemistry. Typically, the DNA encoding the amino acid sequence of a B7-Lpolypeptide will be several hundred nucleotides in length. Nucleic acidslarger than about 100 nucleotides can be synthesized as severalfragments using these methods. The fragments can then be ligatedtogether to form the full-length nucleotide sequence of a B7-L gene.Usually, the DNA fragment encoding the amino-terminus of the polypeptidewill have an ATG, which encodes a methionine residue. This methioninemay or may not be present on the mature form of the B7-L polypeptide,depending on whether the polypeptide produced in the host cell isdesigned to be secreted from that cell. Other methods known to theskilled artisan may be used as well.

In certain embodiments, nucleic acid variants contain codons which havebeen altered for optimal expression of a B7-L polypeptide in a givenhost cell. Particular codon alterations will depend upon the B7-Lpolypeptide and host cell selected for expression. Such “codonoptimization” can be carried out by a variety of methods, for example,by selecting codons which are preferred for use in highly expressedgenes in a given host cell. Computer algorithms which incorporate codonfrequency tables such as “Eco_high.Cod” for codon preference of highlyexpressed bacterial genes may be used and are provided by the Universityof Wisconsin Package Version 9.0 (Genetics Computer Group, Madison,Wis.). Other useful codon frequency tables include “Celegans_high.cod,”“Celegans_low.cod,” “Drosophila_high.cod,” “Human_high.cod,”“Maize_high.cod,” and “Yeast_high.cod.”

In some cases, it may be desirable to prepare nucleic acid moleculesencoding B7-L polypeptide variants. Nucleic acid molecules encodingvariants may be produced using site directed mutagenesis, PCRamplification, or other appropriate methods, where the primer(s) havethe desired point mutations (see Sambrook et al., supra, and Ausubel etal., supra, for descriptions of mutagenesis techniques). Chemicalsynthesis using methods described by Engels et al., supra, may also beused to prepare such variants. Other methods known to the skilledartisan may be used as well.

Vectors and Host Cells

A nucleic acid molecule encoding the amino acid sequence of a B7-Lpolypeptide is inserted into an appropriate expression vector usingstandard ligation techniques. The vector is typically selected to befunctional in the particular host cell employed (i.e., the vector iscompatible with the host cell machinery such that amplification of thegene and/or expression of the gene can occur). A nucleic acid moleculeencoding the amino acid sequence of a B7-L polypeptide may beamplified/expressed in prokaryotic, yeast, insect (baculovirus systems)and/or eukaryotic host cells. Selection of the host cell will depend inpart on whether a B7-L polypeptide is to be post-translationallymodified (e.g., glycosylated and/or phosphorylated). If so, yeast,insect, or mammalian host cells are preferable. For a review ofexpression vectors, see Meth. Enz., vol. 185 (D. V. Goeddel, ed.,Academic Press 1990).

Typically, expression vectors used in any of the host cells will containsequences for plasmid maintenance and for cloning and expression ofexogenous nucleotide sequences. Such sequences, collectively referred toas “flanking sequences” in certain embodiments will typically includeone or more of the following nucleotide sequences: a promoter, one ormore enhancer sequences, an origin of replication, a transcriptionaltermination sequence, a complete intron sequence containing a donor andacceptor splice site, a sequence encoding a leader sequence forpolypeptide secretion, a ribosome binding site, a polyadenylationsequence, a polylinker region for inserting the nucleic acid encodingthe polypeptide to be expressed, and a selectable marker element. Eachof these sequences is discussed below.

Optionally, the vector may contain a “tag”-encoding sequence, i.e., anoligonucleotide molecule located at the 5′ or 3′ end of the B7-Lpolypeptide coding sequence; the oligonucleotide sequence encodespolyHis (such as hexaHis), or another “tag” such as FLAG, HA(hemaglutinin influenza virus), or myc for which commercially availableantibodies exist. This tag is typically fused to the polypeptide uponexpression of the polypeptide, and can serve as a means for affinitypurification of the B7-L polypeptide from the host cell. Affinitypurification can be accomplished, for example, by column chromatographyusing antibodies against the tag as an affinity matrix. Optionally, thetag can subsequently be removed from the purified B7-L polypeptide byvarious means such as using certain peptidases for cleavage.

Flanking sequences may be homologous (i.e., from the same species and/orstrain as the host cell), heterologous (i.e., from a species other thanthe host cell species or strain), hybrid (i.e., a combination offlanking sequences from more than one source), or synthetic, or theflanking sequences may be native sequences that normally function toregulate B7-L polypeptide expression. As such, the source of a flankingsequence may be any prokaryotic or eukaryotic organism, any vertebrateor invertebrate organism, or any plant, provided that the flankingsequence is functional in, and can be activated by, the host cellmachinery.

Flanking sequences useful in the vectors of this invention may beobtained by any of several methods well known in the art. Typically,flanking sequences useful herein—other than the B7-L gene flankingsequences—will have been previously identified by mapping and/or byrestriction endonuclease digestion and can thus be isolated from theproper tissue source using the appropriate restriction endonucleases. Insome cases, the full nucleotide sequence of a flanking sequence may beknown. Here, the flanking sequence may be synthesized using the methodsdescribed herein for nucleic acid synthesis or cloning.

Where all or only a portion of the flanking sequence is known, it may beobtained using PCR and/or by screening a genomic library with a suitableoligonucleotide and/or flanking sequence fragment from the same oranother species. Where the flanking sequence is not known, a fragment ofDNA containing a flanking sequence may be isolated from a larger pieceof DNA that may contain, for example, a coding sequence or even anothergene or genes. Isolation may be accomplished by restriction endonucleasedigestion to produce the proper DNA fragment followed by isolation usingagarose gel purification, Qiagen® column chromatography (Chatsworth,Calif.), or other methods known to the skilled artisan. The selection ofsuitable enzymes to accomplish this purpose will be readily apparent toone of ordinary skill in the art.

An origin of replication is typically a part of those prokaryoticexpression vectors purchased commercially, and the origin aids in theamplification of the vector in a host cell. Amplification of the vectorto a certain copy number can, in some cases, be important for theoptimal expression of a B7-L polypeptide. If the vector of choice doesnot contain an origin of replication site, one may be chemicallysynthesized based on a known sequence, and ligated into the vector. Forexample, the origin of replication from the plasmid pBR322 (New EnglandBiolabs, Beverly, Mass.) is suitable for most gram-negative bacteria andvarious origins (e.g., SV40, polyoma, adenovirus, vesicular stomatitusvirus (VSV), or papillomaviruses such as HPV or BPV) are useful forcloning vectors in mammalian cells. Generally, the origin of replicationcomponent is not needed for mammalian expression vectors (for example,the SV40 origin is often used only because it contains the earlypromoter).

A transcription termination sequence is typically located 3′ of the endof a polypeptide coding region and serves to terminate transcription.Usually, a transcription termination sequence in prokaryotic cells is aG-C rich fragment followed by a poly-T sequence. While the sequence iseasily cloned from a library or even purchased commercially as part of avector, it can also be readily synthesized using methods for nucleicacid synthesis such as those described herein.

A selectable marker gene element encodes a protein necessary for thesurvival and growth of a host cell grown in a selective culture medium.Typical selection marker genes encode proteins that (a) conferresistance to antibiotics or other toxins, e.g., ampicillin,tetracycline, or kanamycin for prokaryotic host cells; (b) complementauxotrophic deficiencies of the cell; or (c) supply critical nutrientsnot available from complex media. Preferred selectable markers are thekanamycin resistance gene, the ampicillin resistance gene, and thetetracycline resistance gene. A neomycin resistance gene may also beused for selection in prokaryotic and eukaryotic host cells.

Other selection genes may be used to amplify the gene that will beexpressed. Amplification is the process wherein genes that are ingreater demand for the production of a protein critical for growth arereiterated in tandem within the chromosomes of successive generations ofrecombinant cells. Examples of suitable selectable markers for mammaliancells include dihydrofolate reductase (DHFR) and thymidine kinase. Themammalian cell transformants are placed under selection pressure whereinonly the transformants are uniquely adapted to survive by virtue of theselection gene present in the vector. Selection pressure is imposed byculturing the transformed cells under conditions in which theconcentration of selection agent in the medium is successively changed,thereby leading to the amplification of both the selection gene and theDNA that encodes a B7-L polypeptide. As a result, increased quantitiesof B7-L polypeptide are synthesized from the amplified DNA.

A ribosome binding site is usually necessary for translation initiationof mRNA and is characterized by a Shine-Dalgarno sequence (prokaryotes)or a Kozak sequence (eukaryotes). The element is typically located 3′ tothe promoter and 5′ to the coding sequence of a B7-L polypeptide to beexpressed. The Shine-Dalgarno sequence is varied but is typically apolypurine (i.e., having a high A-G content). Many Shine-Dalgarnosequences have been identified, each of which can be readily synthesizedusing methods set forth herein and used in a prokaryotic vector.

A leader, or signal, sequence may be used to direct a B7-L polypeptideout of the host cell. Typically, a nucleotide sequence encoding thesignal sequence is positioned in the coding region of a B7-L nucleicacid molecule, or directly at the 5′ end of a B7-L polypeptide codingregion. Many signal sequences have been identified, and any of thosethat are functional in the selected host cell may be used in conjunctionwith a B7-L nucleic acid molecule. Therefore, a signal sequence may behomologous (naturally occurring) or heterologous to the B7-L nucleicacid molecule. Additionally, a signal sequence may be chemicallysynthesized using methods described herein. In most cases, the secretionof a B7-L polypeptide from the host cell via the presence of a signalpeptide will result in the removal of the signal peptide from thesecreted B7-L polypeptide. The signal sequence may be a component of thevector, or it may be a part of a B7-L nucleic acid molecule that isinserted into the vector.

Included within the scope of this invention is the use of either anucleotide sequence encoding a native B7-L polypeptide signal sequencejoined to a B7-L polypeptide coding region or a nucleotide sequenceencoding a heterologous signal sequence joined to a B7-L polypeptidecoding region. The heterologous signal sequence selected should be onethat is recognized and processed, i.e., cleaved by a signal peptidase,by the host cell. For prokaryotic host cells that do not recognize andprocess the native B7-L polypeptide signal sequence, the signal sequenceis substituted by a prokaryotic signal sequence selected, for example,from the group of the alkaline phosphatase, penicillinase, orheat-stable enterotoxin II leaders. For yeast secretion, the native B7-Lpolypeptide signal sequence may be substituted by the yeast invertase,alpha factor, or acid phosphatase leaders. In mammalian cell expressionthe native signal sequence is satisfactory, although other mammaliansignal sequences may be suitable.

In some cases, such as where glycosylation is desired in a eukaryotichost cell expression system, one may manipulate the various presequencesto improve glycosylation or yield. For example, one may alter thepeptidase cleavage site of a particular signal peptide, or addpro-sequences, which also may affect glycosylation. The final proteinproduct may have, in the −1 position (relative to the first amino acidof the mature protein) one or more additional amino acids incident toexpression, which may not have been totally removed. For example, thefinal protein product may have one or two amino acid residues found inthe peptidase cleavage site, attached to the amino-terminus.Alternatively, use of some enzyme cleavage sites may result in aslightly truncated form of the desired B7-L polypeptide, if the enzymecuts at such area within the mature polypeptide.

In many cases, transcription of a nucleic acid molecule is increased bythe presence of one or more introns in the vector; this is particularlytrue where a polypeptide is produced in eukaryotic host cells,especially mammalian host cells. The introns used may be naturallyoccurring within the B7-L gene especially where the gene used is afull-length genomic sequence or a fragment thereof. Where the intron isnot naturally occurring within the gene (as for most cDNAs), the intronmay be obtained from another source. The position of the intron withrespect to flanking sequences and the B7-L gene is generally important,as the intron must be transcribed to be effective. Thus, when a B7-LcDNA molecule is being transcribed, the preferred position for theintron is 3′ to the transcription start site and 5′ to the poly-Atranscription termination sequence. Preferably, the intron or intronswill be located on one side or the other (i.e., 5′ or 3′) of the cDNAsuch that it does not interrupt the coding sequence. Any intron from anysource, including viral, prokaryotic and eukaryotic (plant or animal)organisms, may be used to practice this invention, provided that it iscompatible with the host cell into which it is inserted. Also includedherein are synthetic introns. Optionally, more than one intron may beused in the vector.

The expression and cloning vectors of the present invention willtypically contain a promoter that is recognized by the host organism andoperably linked to the molecule encoding the B7-L polypeptide. Promotersare untranscribed sequences located upstream (i.e., 5′) to the startcodon of a structural gene (generally within about 100 to 1000 bp) thatcontrol the transcription of the structural gene. Promoters areconventionally grouped into one of two classes: inducible promoters andconstitutive promoters. Inducible promoters initiate increased levels oftranscription from DNA under their control in response to some change inculture conditions, such as the presence or absence of a nutrient or achange in temperature. Constitutive promoters, on the other hand,initiate continual gene product production; that is, there is little orno control over gene expression. A large number of promoters, recognizedby a variety of potential host cells, are well known. A suitablepromoter is operably linked to the DNA encoding B7-L polypeptide byremoving the promoter from the source DNA by restriction enzymedigestion and inserting the desired promoter sequence into the vector.The native B7-L promoter sequence may be used to direct amplificationand/or expression of a B7-L nucleic acid molecule. A heterologouspromoter is preferred, however, if it permits greater transcription andhigher yields of the expressed protein as compared to the nativepromoter, and if it is compatible with the host cell system that hasbeen selected for use.

Promoters suitable for use with prokaryotic hosts include thebeta-lactamase and lactose promoter systems; alkaline phosphatase; atryptophan (trp) promoter system; and hybrid promoters such as the tacpromoter. Other known bacterial promoters are also suitable. Theirsequences have been published, thereby enabling one skilled in the artto ligate them to the desired DNA sequence, using linkers or adapters asneeded to supply any useful restriction sites.

Suitable promoters for use with yeast hosts are also well known in theart. Yeast enhancers are advantageously used with yeast promoters.Suitable promoters for use with mammalian host cells are well known andinclude, but are not limited to, those obtained from the genomes ofviruses such as polyoma virus, fowlpox virus, adenovirus (such asAdenovirus 2), bovine papilloma virus, avian sarcoma virus,cytomegalovirus, retroviruses, hepatitis-B virus and most preferablySimian Virus 40 (SV40). Other suitable mammalian promoters includeheterologous mammalian promoters, for example, heat-shock promoters andthe actin promoter.

Additional promoters which may be of interest in controlling B7-L geneexpression include, but are not limited to: the SV40 early promoterregion (Bernoist and Chambon, 1981, Nature 290:304-10); the CMVpromoter; the promoter contained in the 3′ long terminal repeat of Roussarcoma virus (Yamamoto, et al., 1980, Cell 22:787-97); the herpesthymidine kinase promoter (Wagner et al., 1981, Proc. Natl. Acad. Sci.U.S.A. 78:1444-45); the regulatory sequences of the metallothionine gene(Brinster et al., 1982, Nature 296:39-42); prokaryotic expressionvectors such as the beta-lactamase promoter (Villa-Kamaroff et al.,1978, Proc. Natl. Acad. Sci. U.S.A., 75:3727-31); or the tac promoter(DeBoer et al., 1983, Proc. Natl. Acad. Sci. U.S.A., 80:21-25). Also ofinterest are the following animal transcriptional control regions, whichexhibit tissue specificity and have been utilized in transgenic animals:the elastase I gene control region which is active in pancreatic acinarcells (Swift et al., 1984, Cell 38:639-46; Ornitz et al., 1986, ColdSpring Harbor Symp. Quant. Biol. 50:399-409 (1986); MacDonald, 1987,Hepatology 7:425-515); the insulin gene control region which is activein pancreatic beta cells (Hanahan, 1985, Nature 315:115-22); theimmunoglobulin gene control region which is active in lymphoid cells(Grosschedl et al., 1984, Cell 38:647-58; Adames et al., 1985, Nature318:533-38; Alexander et al., 1987, Mol. Cell. Biol., 7:1436-44); themouse mammary tumor virus control region which is active in testicular,breast, lymphoid and mast cells (Leder et al., 1986, Cell 45:485-95);the albumin gene control region which is active in liver (Pinkert etal., 1987, Genes and Devel. 1:268-76); the alpha-feto-protein genecontrol region which is active in liver (Krumlauf et al., 1985, Mol.Cell. Biol., 5:1639-48; Hammer et al., 1987, Science 235:53-58); thealpha 1-antitrypsin gene control region which is active in the liver(Kelsey et al., 1987, Genes and Devel. 1:161-71); the beta-globin genecontrol region which is active in myeloid cells (Mogram et al., 1985,Nature 315:338-40; Kollias et al., 1986, Cell 46:89-94); the myelinbasic protein gene control region which is active in oligodendrocytecells in the brain (Readhead et al., 1987, Cell 48:703-12); the myosinlight chain-2 gene control region which is active in skeletal muscle(Sani, 1985, Nature 314:283-86); and the gonadotropic releasing hormonegene control region which is active in the hypothalamus (Mason et al.,1986, Science 234:1372-78).

An enhancer sequence may be inserted into the vector to increase thetranscription of a DNA encoding a B7-L polypeptide of the presentinvention by higher eukaryotes. Enhancers are cis-acting elements ofDNA, usually about 10-300 bp in length, that act on the promoter toincrease transcription. Enhancers are relatively orientation andposition independent. They have been found 5′ and 3′ to thetranscription unit. Several enhancer sequences available from mammaliangenes are known (e.g., globin, elastase, albumin, alpha-feto-protein andinsulin). Typically, however, an enhancer from a virus will be used. TheSV40 enhancer, the cytomegalovirus early promoter enhancer, the polyomaenhancer, and adenovirus enhancers are exemplary enhancing elements forthe activation of eukaryotic promoters. While an enhancer may be splicedinto the vector at a position 5′ or 3′ to a B7-L nucleic acid molecule,it is typically located at a site 5′ from the promoter.

Expression vectors of the invention may be constructed from a startingvector such as a commercially available vector. Such vectors may or maynot contain all of the desired flanking sequences. Where one or more ofthe flanking sequences described herein are not already present in thevector, they may be individually obtained and ligated into the vector.Methods used for obtaining each of the flanking sequences are well knownto one skilled in the art.

Preferred vectors for practicing this invention are those that arecompatible with bacterial, insect, and mammalian host cells. Suchvectors include, inter alia, pCRII, pCR3, and pcDNA3.1 (Invitrogen, SanDiego, Calif.), pBSII (Stratagene, La Jolla, Calif.), pET15 (Novagen,Madison, Wis.), pGEX (Pharmacia Biotech, Piscataway, N.J.), pEGFP-N2(Clontech, Palo Alto, Calif.), pETL (BlueBacII, Invitrogen), pDSR-alpha(International Pub. No. WO 90/14363) and pFastBacDual (Gibco-BRL, GrandIsland, N.Y.).

Additional suitable vectors include, but are not limited to, cosmids,plasmids, or modified viruses, but it will be appreciated that thevector system must be compatible with the selected host cell. Suchvectors include, but are not limited to plasmids such as Bluescript®plasmid derivatives (a high copy number ColE1-based phagemid; StratageneCloning Systems, La Jolla Calif.), PCR cloning plasmids designed forcloning Taq-amplified PCR products (e.g., TOPO™ TA Cloning® Kit andPCR2.1® plasmid derivatives; Invitrogen), and mammalian, yeast or virusvectors such as a baculovirus expression system (pBacPAK plasmidderivatives; Clontech).

After the vector has been constructed and a nucleic acid moleculeencoding a B7-L polypeptide has been inserted into the proper site ofthe vector, the completed vector may be inserted into a suitable hostcell for amplification and/or polypeptide expression. The transformationof an expression vector for a B7-L polypeptide into a selected host cellmay be accomplished by well known methods including methods such astransfection, infection, calcium chloride, electroporation,microinjection, lipofection, DEAE-dextran method, or other knowntechniques. The method selected will in part be a function of the typeof host cell to be used. These methods and other suitable methods arewell known to the skilled artisan, and are set forth, for example, inSambrook et al., supra.

Host cells may be prokaryotic host cells (such as E. coli) or eukaryotichost cells (such as a yeast, insect, or vertebrate cell). The host cell,when cultured under appropriate conditions, synthesizes a B7-Lpolypeptide that can subsequently be collected from the culture medium(if the host cell secretes it into the medium) or directly from the hostcell producing it (if it is not secreted). The selection of anappropriate host cell will depend upon various factors, such as desiredexpression levels, polypeptide modifications that are desirable ornecessary for activity (such as glycosylation or phosphorylation) andease of folding into a biologically active molecule.

A number of suitable host cells are known in the art and many areavailable from the American Type Culture Collection (ATCC), Manassas,Va. Examples include, but are not limited to, mammalian cells, such asChinese hamster ovary cells (CHO), CHO DHFR(−) cells (Urlaub et al.,1980, Proc. Natl. Acad. Sci. U.S.A. 97:4216-20), human embryonic kidney(HEK) 293 or 293T cells, or 3T3 cells. The selection of suitablemammalian host cells and methods for transformation, culture,amplification, screening, product production, and purification are knownin the art. Other suitable mammalian cell lines, are the monkey COS-1and COS-7 cell lines, and the CV-1 cell line. Further exemplarymammalian host cells include primate cell lines and rodent cell lines,including transformed cell lines. Normal diploid cells, cell strainsderived from in vitro culture of primary tissue, as well as primaryexplants, are also suitable. Candidate cells may be genotypicallydeficient in the selection gene, or may contain a dominantly actingselection gene. Other suitable mammalian cell lines include but are notlimited to, mouse neuroblastoma N2A cells, HeLa, mouse L-929 cells, 3T3lines derived from Swiss, Balb-c or NIH mice, BHK or HaK hamster celllines. Each of these cell lines is known by and available to thoseskilled in the art of protein expression.

Similarly useful as host cells suitable for the present invention arebacterial cells. For example, the various strains of E. coli (e.g.,HB101, DHSα, DH10, and MC1061) are well-known as host cells in the fieldof biotechnology. Various strains of B. subtilis, Pseudomonas spp.,other Bacillus spp., Streptomyces spp., and the like may also beemployed in this method.

Many strains of yeast cells known to those skilled in the art are alsoavailable as host cells for the expression of the polypeptides of thepresent invention. Preferred yeast cells include, for example,Saccharomyces cerivisae and Pichia pastoris.

Additionally, where desired, insect cell systems may be utilized in themethods of the present invention. Such systems are described, forexample, in Kitts et al., 1993, Biotechniques, 14:810-17; Lucklow, 1993,Curr. Opin. Biotechnol. 4:564-72; and Lucklow et al., 1993, J. Virol.,67:4566-79. Preferred insect cells are Sf-9 and Hi5 (Invitrogen).

One may also use transgenic animals to express glycosylated B7-Lpolypeptides. For example, one may use a transgenic milk-producinganimal (a cow or goat, for example) and obtain the present glycosylatedpolypeptide in the animal milk. One may also use plants to produce B7-Lpolypeptides, however, in general, the glycosylation occurring in plantsis different from that produced in mammalian cells, and may result in aglycosylated product which is not suitable for human therapeutic use.

Polypeptide Production

Host cells comprising a B7-L polypeptide expression vector may becultured using standard media well known to the skilled artisan. Themedia will usually contain all nutrients necessary for the growth andsurvival of the cells. Suitable media for culturing E. coli cellsinclude, for example, Luria Broth (LB) and/or Terrific Broth (TB).Suitable media for culturing eukaryotic cells include Roswell ParkMemorial Institute medium 1640 (RP EMI 1640), Minimal Essential Medium(MEM) and/or Dulbecco's Modified Eagle Medium (DMEM), all of which maybe supplemented with serum and/or growth factors as necessary for theparticular cell line being cultured. A suitable medium for insectcultures is Grace's medium supplemented with yeastolate, lactalbuminhydrolysate, and/or fetal calf serum as necessary.

Typically, an antibiotic or other compound useful for selective growthof transfected or transformed cells is added as a supplement to themedia. The compound to be used will be dictated by the selectable markerelement present on the plasmid with which the host cell was transformed.For example, where the selectable marker element is kanamycinresistance, the compound added to the culture medium will be kanamycin.Other compounds for selective growth include ampicillin, tetracycline,and neomycin.

The amount of a B7-L polypeptide produced by a host cell can beevaluated using standard methods known in the art. Such methods include,without limitation, Western blot analysis, SDS-polyacrylamide gelelectrophoresis, non-denaturing gel electrophoresis, High PerformanceLiquid Chromatography (HPLC) separation, immunoprecipitation, and/oractivity assays such as DNA binding gel shift assays.

If a B7-L polypeptide has been designed to be secreted from the hostcells, the majority of polypeptide may be found in the cell culturemedium. If however, the B7-L polypeptide is not secreted from the hostcells, it will be present in the cytoplasm and/or the nucleus (foreukaryotic host cells) or in the cytosol (for gram-negative bacteriahost cells).

For a B7-L polypeptide situated in the host cell cytoplasm and/ornucleus (for eukaryotic host cells) or in the cytosol (for bacterialhost cells), the intracellular material (including inclusion bodies forgram-negative bacteria) can be extracted from the host cell using anystandard technique known to the skilled artisan. For example, the hostcells can be lysed to release the contents of the periplasm/cytoplasm byFrench press, homogenization, and/or sonication followed bycentrifugation.

If a B7-L polypeptide has formed inclusion bodies in the cytosol, theinclusion bodies can often bind to the inner and/or outer cellularmembranes and thus will be found primarily in the pellet material aftercentrifugation. The pellet material can then be treated at pH extremesor with a chaotropic agent such as a detergent, guanidine, guanidinederivatives, urea, or urea derivatives in the presence of a reducingagent such as dithiothreitol at alkaline pH or tris carboxyethylphosphine at acid pH to release, break apart, and solubilize theinclusion bodies. The solubilized B7-L polypeptide can then be analyzedusing gel electrophoresis, immunoprecipitation, or the like. If it isdesired to isolate the B7-L polypeptide, isolation may be accomplishedusing standard methods such as those described herein and in Marston etal., 1990, Meth. Enz., 182:264-75.

In some cases, a B7-L polypeptide may not be biologically active uponisolation. Various methods for “refolding” or converting the polypeptideto its tertiary structure and generating disulfide linkages can be usedto restore biological activity. Such methods include exposing thesolubilized polypeptide to a pH usually above 7 and in the presence of aparticular concentration of a chaotrope. The selection of chaotrope isvery similar to the choices used for inclusion body solubilization, butusually the chaotrope is used at a lower concentration and is notnecessarily the same as chaotropes used for the solubilization. In mostcases the refolding/oxidation solution will also contain a reducingagent or the reducing agent plus its oxidized form in a specific ratioto generate a particular redox potential allowing for disulfideshuffling to occur in the formation of the protein's cysteine bridges.Some of the commonly used redox couples include cysteine/cystamine,glutathione (GSH)/dithiobis GSH, cupric chloride,dithiothreitol(DTT)/dithiane DTT, and2-2-mercaptoethanol(bME)/dithio-b(ME). In many instances, a cosolventmay be used or may be needed to increase the efficiency of therefolding, and the more common reagents used for this purpose includeglycerol, polyethylene glycol of various molecular weights, arginine andthe like.

If inclusion bodies are not formed to a significant degree uponexpression of a B7-L polypeptide, then the polypeptide will be foundprimarily in the supernatant after centrifugation of the cellhomogenate. The polypeptide may be further isolated from the supernatantusing methods such as those described herein.

The purification of a B7-L polypeptide from solution can be accomplishedusing a variety of techniques. If the polypeptide has been synthesizedsuch that it contains a tag such as Hexahistidine (B7-Lpolypeptide/hexaHis) or other small peptide such as FLAG (Eastman KodakCo., New Haven, Conn.) or myc (Invitrogen) at either its carboxyl- oramino-terminus, it may be purified in a one-step process by passing thesolution through an affinity column where the column matrix has a highaffinity for the tag.

For example, polyhistidine binds with great affinity and specificity tonickel. Thus, an affinity column of nickel (such as the Qiagen® nickelcolumns) can be used for purification of B7-L polypeptide/polyHis. See,e.g., Current Protocols in Molecular Biology § 10.11.8 (Ausubel et al.,eds., Green Publishers Inc. and Wiley and Sons 1993).

Additionally, B7-L polypeptides may be purified through the use of amonoclonal antibody that is capable of specifically recognizing andbinding to a B7-L polypeptide.

Other suitable procedures for purification include, without limitation,affinity chromatography, immunoaffinity chromatography, ion exchangechromatography, molecular sieve chromatography, HPLC, electrophoresis(including native gel electrophoresis) followed by gel elution, andpreparative isoelectric focusing (“Isoprime” machine/technique, HoeferScientific, San Francisco, Calif.). In some cases, two or morepurification techniques may be combined to achieve increased purity.

B7-L polypeptides may also be prepared by chemical synthesis methods(such as solid phase peptide synthesis) using techniques known in theart such as those set forth by Merrifield et al., 1963, J. Am. Chem.Soc. 85:2149; Houghten et al., 1985, Proc Natl Acad. Sci. USA 82:5132;and Stewart and Young, Solid Phase Peptide Synthesis (Pierce ChemicalCo. 1984). Such polypeptides may be synthesized with or without amethionine on the amino-terminus. Chemically synthesized B7-Lpolypeptides may be oxidized using methods set forth in these referencesto form disulfide bridges. Chemically synthesized B7-L polypeptides areexpected to have comparable biological activity to the correspondingB7-L polypeptides produced recombinantly or purified from naturalsources, and thus may be used interchangeably with a recombinant ornatural B7-L polypeptide.

Another means of obtaining B7-L polypeptide is via purification frombiological samples such as source tissues and/or fluids in which theB7-L polypeptide is naturally found. Such purification can be conductedusing methods for protein purification as described herein. The presenceof the B7-L polypeptide during purification may be monitored, forexample, using an antibody prepared against recombinantly produced B7-Lpolypeptide or peptide fragments thereof.

A number of additional methods for producing nucleic acids andpolypeptides are known in the art, and the methods can be used toproduce polypeptides having specificity for B7-L polypeptide. See, e.g.,Roberts et al., 1997, Proc. Natl. Acad. Sci. U.S.A. 94:12297-303, whichdescribes the production of fusion proteins between an mRNA and itsencoded peptide. See also, Roberts, 1999, Curr. Opin. Chem. Biol.3:268-73. Additionally, U.S. Pat. No. 5,824,469 describes methods forobtaining oligonucleotides capable of carrying out a specific biologicalfunction. The procedure involves generating a heterogeneous pool ofoligonucleotides, each having a 5′ randomized sequence, a centralpreselected sequence, and a 3′ randomized sequence. The resultingheterogeneous pool is introduced into a population of cells that do notexhibit the desired biological function. Subpopulations of the cells arethen screened for those that exhibit a predetermined biologicalfunction. From that subpopulation, oligonucleotides capable of carryingout the desired biological function are isolated.

U.S. Pat. Nos. 5,763,192; 5,814,476; 5,723,323; and 5,817,483 describeprocesses for producing peptides or polypeptides. This is done byproducing stochastic genes or fragments thereof, and then introducingthese genes into host cells which produce one or more proteins encodedby the stochastic genes. The host cells are then screened to identifythose clones producing peptides or polypeptides having the desiredactivity.

Another method for producing peptides or polypeptides is described inInternational Pub. No. WO99/15650, filed by Athersys, Inc. Known as“Random Activation of Gene Expression for Gene Discovery” (RAGE-GD), theprocess involves the activation of endogenous gene expression orover-expression of a gene by in situ recombination methods. For example,expression of an endogenous gene is activated or increased byintegrating a regulatory sequence into the target cell that is capableof activating expression of the gene by non-homologous or illegitimaterecombination. The target DNA is first subjected to radiation, and agenetic promoter inserted. The promoter eventually locates a break atthe front of a gene, initiating transcription of the gene. This resultsin expression of the desired peptide or polypeptide.

It will be appreciated that these methods can also be used to createcomprehensive B7-L polypeptide expression libraries, which cansubsequently be used for high throughput phenotypic screening in avariety of assays, such as biochemical assays, cellular assays, andwhole organism assays (e.g., plant, mouse, etc.).

Synthesis

It will be appreciated by those skilled in the art that the nucleic acidand polypeptide molecules described herein may be produced byrecombinant and other means.

Selective Binding Agents

The term “selective binding agent” refers to a molecule that hasspecificity for one or more B7-L polypeptides. Suitable selectivebinding agents include, but are not limited to, antibodies andderivatives thereof, polypeptides, and small molecules. Suitableselective binding agents may be prepared using methods known in the art.An exemplary B7-L polypeptide selective binding agent of the presentinvention is capable of binding a certain portion of the B7-Lpolypeptide thereby inhibiting the binding of the polypeptide to a B7-Lpolypeptide receptor.

Selective binding agents such as antibodies and antibody fragments thatbind B7-L polypeptides are within the scope of the present invention.The antibodies may be polyclonal including monospecific polyclonal;monoclonal (MAbs); recombinant; chimeric; humanized, such ascomplementarity-determining region (CDR)-grafted; human; single chain;and/or bispecific; as well as fragments; variants; or derivativesthereof. Antibody fragments include those portions of the antibody thatbind to an epitope on the B7-L polypeptide. Examples of such fragmentsinclude Fab and F(ab′) fragments generated by enzymatic cleavage offull-length antibodies. Other binding fragments include those generatedby recombinant DNA techniques, such as the expression of recombinantplasmids containing nucleic acid sequences encoding antibody variableregions.

Polyclonal antibodies directed toward a B7-L polypeptide generally areproduced in animals (e.g., rabbits or mice) by means of multiplesubcutaneous or intraperitoneal injections of B7-L polypeptide and anadjuvant. It may be useful to conjugate a B7-L polypeptide to a carrierprotein that is immunogenic in the species to be immunized, such askeyhole limpet hemocyanin, serum, albumin, bovine thyroglobulin, orsoybean trypsin inhibitor. Also, aggregating agents such as alum areused to enhance the immune response. After immunization, the animals arebled and the serum is assayed for anti-B7-L antibody titer.

Monoclonal antibodies directed toward B7-L polypeptides are producedusing any method that provides for the production of antibody moleculesby continuous cell lines in culture. Examples of suitable methods forpreparing monoclonal antibodies include the hybridoma methods of Kohleret al., 1975, Nature 256:495-97 and the human B-cell hybridoma method(Kozbor, 1984, J. Immunol. 133:3001; Brodeur et al., Monoclonal AntibodyProduction Techniques and Applications 51-63 (Marcel Dekker, Inc.,1987). Also provided by the invention are hybridoma cell lines thatproduce monoclonal antibodies reactive with B7-L polypeptides.

Monoclonal antibodies of the invention may be modified for use astherapeutics. One embodiment is a “chimeric” antibody in which a portionof the heavy (H) and/or light (L) chain is identical with or homologousto a corresponding sequence in antibodies derived from a particularspecies or belonging to a particular antibody class or subclass, whilethe remainder of the chain(s) is/are identical with or homologous to acorresponding sequence in antibodies derived from another species orbelonging to another antibody class or subclass. Also included arefragments of such antibodies, so long as they exhibit the desiredbiological activity. See U.S. Pat. No. 4,816,567; Morrison et al., 1985,Proc. Natl. Acad. Sci. 81:6851-55.

In another embodiment, a monoclonal antibody of the invention is a“humanized” antibody. Methods for humanizing non-human antibodies arewell known in the art. See U.S. Pat. Nos. 5,585,089 and 5,693,762.Generally, a humanized antibody has one or more amino acid residuesintroduced into it from a source that is non-human. Humanization can beperformed, for example, using methods described in the art (Jones etal., 1986, Nature 321:522-25; Riechmann et al., 1998, Nature 332:323-27;Verhoeyen et al., 1988, Science 239:1534-36), by substituting at least aportion of a rodent complementarity-determining region for thecorresponding regions of a human antibody.

Also encompassed by the invention are human antibodies that bind. B7-Lpolypeptides. Using transgenic animals (e.g., mice) that are capable ofproducing a repertoire of human antibodies in the absence of endogenousimmunoglobulin production such antibodies are produced by immunizationwith a B7-L polypeptide antigen (i.e., having at least 6 contiguousamino acids), optionally conjugated to a carrier. See, e.g., Jakobovitset al., 1993, Proc. Natl. Acad. Sci. 90:2551-55; Jakobovits et al.,1993, Nature 362:255-58; Bruggermann et al., 1993, Year in Immuno. 7:33.In one method, such transgenic animals are produced by incapacitatingthe endogenous loci encoding the heavy and light immunoglobulin chainstherein, and inserting loci encoding human heavy and light chainproteins into the genome thereof. Partially modified animals (i.e.,those having less than the full complement of modifications) are thencross-bred to obtain an animal having all of the desired immune systemmodifications. When administered an immunogen, these transgenic animalsproduce antibodies with human (rather than, e.g., murine) amino acidsequences, including variable regions that are immunospecific for theseantigens. See International App. Nos. PCT/US96/05928 and PCT/US93/06926.Additional methods are described in U.S. Pat. No. 5,545,807,International App. Nos. PCT/US91/245 and PCT/GB89/01207, and in EuropeanPatent Nos. 546073B1 and 546073A1. Human antibodies can also be producedby the expression of recombinant DNA in host cells or by expression inhybridoma cells as described herein.

In an alternative embodiment, human antibodies can also be produced fromphage-display libraries (Hoogenboom et al., 1991, J. Mol. Biol. 227:381;Marks et al., 1991, J. Mol. Biol. 222:581). These processes mimic immuneselection through the display of antibody repertoires on the surface offilamentous bacteriophage, and subsequent selection of phage by theirbinding to an antigen of choice. One such technique is described inInternational App. No. PCT/US98/17364, which describes the isolation ofhigh affinity and functional agonistic antibodies for MPL- andmsk-receptors using such an approach.

Chimeric, CDR grafted, and humanized antibodies are typically producedby recombinant methods. Nucleic acids encoding the antibodies areintroduced into host cells and expressed using materials and proceduresdescribed herein. In a preferred embodiment, the antibodies are producedin mammalian host cells, such as CHO cells. Monoclonal (e.g., human)antibodies may be produced by the expression of recombinant DNA in hostcells or by expression in hybridoma cells as described herein.

The anti-B7-L antibodies of the invention may be employed in any knownassay method, such as competitive binding assays, direct and indirectsandwich assays, and immunoprecipitation assays (Sola, MonoclonalAntibodies: A Manual of Techniques 147-158 (CRC Press, Inc., 1987)) forthe detection and quantitation of B7-L polypeptides. The antibodies willbind B7-L polypeptides with an affinity, that is appropriate for theassay method being employed.

For diagnostic applications, in certain embodiments, anti-B7-Lantibodies may be labeled with a detectable moiety. The detectablemoiety can be any one that is capable of producing, either directly orindirectly, a detectable signal. For example, the detectable moiety maybe a radioisotope, such as ³H, ¹⁴C ³²P, ³⁵S, ¹²⁵I, ⁹⁹Tc, ¹¹¹In, or ⁶⁷Ga;a fluorescent or chemiluminescent compound, such as fluoresceinisothiocyanate, rhodamine, or luciferin; or an enzyme, such as alkalinephosphatase, β-galactosidase, or horseradish peroxidase (Bayer, et al.,1990, Meth. Enz. 184:138-63).

Competitive binding assays rely on the ability of a labeled standard(e.g., a B7-L polypeptide, or an immunologically reactive portionthereof) to compete with the test sample analyte (an B7-L polypeptide)for binding with a limited amount of anti-B7-L antibody. The amount of aB7-L polypeptide in the test sample is inversely proportional to theamount of standard that becomes bound to the antibodies. To facilitatedetermining the amount of standard that becomes bound, the antibodiestypically are insolubilized before or after the competition, so that thestandard and analyte that are bound to the antibodies may convenientlybe separated from the standard and analyte that remain unbound.

Sandwich assays typically involve the use of two antibodies, eachcapable of binding to a different immunogenic portion, or epitope, ofthe protein to be detected and/or quantitated. In a sandwich assay, thetest sample analyte is typically bound by a first antibody that isimmobilized on a solid support, and thereafter a second antibody bindsto the analyte, thus forming an insoluble three-part complex. See, e.g.,U.S. Pat. No. 4,376,110. The second antibody may itself be labeled witha detectable moiety (direct sandwich assays) or may be measured using ananti-immunoglobulin antibody that is labeled with a detectable moiety(indirect sandwich assays). For example, one type of sandwich assay isan enzyme-linked immunosorbent assay (ELISA), in which case thedetectable moiety is an enzyme.

The selective binding agents, including anti-B7-L antibodies, are alsouseful for in vivo imaging. An antibody labeled with a detectable moietymay be administered to an animal, preferably into the bloodstream, andthe presence and location of the labeled antibody in the host assayed.The antibody may be labeled with any moiety that is detectable in ananimal, whether by nuclear magnetic resonance, radiology, or otherdetection means known in the art.

Selective binding agents of the invention, including antibodies, may beused as therapeutics. These therapeutic agents are generally agonists orantagonists, in that they either enhance or reduce, respectively, atleast one of the biological activities of a B7-L polypeptide. In oneembodiment, antagonist antibodies of the invention are antibodies orbinding fragments thereof which are capable of specifically binding to aB7-L polypeptide and which are capable of inhibiting or eliminating thefunctional activity of a B7-L polypeptide in vivo or in vitro. Inpreferred embodiments, the selective binding agent, e.g., an antagonistantibody, will inhibit the functional activity of a B7-L polypeptide byat least about 50%, and preferably by at least about 80%. In anotherembodiment, the selective binding agent may be an anti-B7-L polypeptideantibody that is capable of interacting with a B7-L polypeptide bindingpartner (a ligand or receptor) thereby inhibiting or eliminating B7-Lpolypeptide activity in vitro or in vivo. Selective binding agents,including agonist and antagonist anti-B7-L polypeptide antibodies, areidentified by screening assays that are well known in the art.

The invention also relates to a kit comprising B7-L selective bindingagents (such as antibodies) and other reagents useful for detecting B7-Lpolypeptide levels in biological samples. Such reagents may include adetectable label, blocking serum, positive and negative control samples,and detection reagents.

Microarrays

It will be appreciated that DNA microarray technology can be utilized inaccordance with the present invention. DNA microarrays are miniature,high-density arrays of nucleic acids positioned on a solid support, suchas glass. Each cell or element within the array contains numerous copiesof a single nucleic acid species that acts as a target for hybridizationwith a complementary nucleic acid sequence (e.g., mRNA). In expressionprofiling using DNA microarray technology, mRNA is first extracted froma cell or tissue sample and then converted enzymatically tofluorescently labeled cDNA. This material is hybridized to themicroarray and unbound cDNA is removed by washing. The expression ofdiscrete genes represented on the array is then visualized byquantitating the amount of labeled cDNA that is specifically bound toeach target nucleic acid molecule. In this way, the expression ofthousands of genes can be quantitated in a high throughput, parallelmanner from a single sample of biological material.

This high throughput expression profiling has a broad range ofapplications with respect to the B7-L molecules of the invention,including, but not limited to: the identification and validation of B7-Ldisease-related genes as targets for therapeutics; molecular toxicologyof related B7-L molecules and inhibitors thereof; stratification ofpopulations and generation of surrogate markers for clinical trials; andenhancing related B7-L polypeptide small molecule drug discovery byaiding in the identification of selective compounds in high throughputscreens.

Chemical Derivatives

Chemically modified derivatives of B7-L polypeptides may be prepared byone skilled in the art, given the disclosures described herein. B7-Lpolypeptide derivatives are modified in a manner that isdifferent—either in the type or location of the molecules naturallyattached to the polypeptide. Derivatives may include molecules formed bythe deletion of one or more naturally-attached chemical groups. Thepolypeptide comprising the amino acid sequence of SEQ ID NO: 2, or otherB7-L polypeptide, may be modified by the covalent attachment of one ormore polymers. For example, the polymer selected is typicallywater-soluble so that the protein to which it is attached does notprecipitate in an aqueous environment, such as a physiologicalenvironment. Included within the scope of suitable polymers is a mixtureof polymers. Preferably, for therapeutic use of the end-productpreparation, the polymer will be pharmaceutically acceptable.

The polymers each may be of any molecular weight and may be branched orunbranched. The polymers each typically have an average molecular weightof between about 2 kDa to about 100 kDa (the term “about” indicatingthat in preparations of a water-soluble polymer, some molecules willweigh more, some less, than the stated molecular weight). The averagemolecular weight of each polymer is preferably between about 5 kDa andabout 50 kDa, more preferably between about 12 kDa and about 40 kDa andmost preferably between about 20 kDa and about 35 kDa.

Suitable water-soluble polymers or mixtures thereof include, but are notlimited to, N-linked or O-linked carbohydrates, sugars, phosphates,polyethylene glycol (PEG) (including the forms of PEG that have beenused to derivatize proteins, including mono-(C₁-C₁₀), alkoxy-, oraryloxy-polyethylene glycol), monomethoxy-polyethylene glycol, dextran(such as low molecular weight dextran of, for example, about 6 kD),cellulose, or other carbohydrate based polymers, poly-(N-vinylpyrrolidone) polyethylene glycol, propylene glycol homopolymers,polypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols(e.g., glycerol), and polyvinyl alcohol. Also encompassed by the presentinvention are bifunctional crosslinking molecules that may be used toprepare covalently attached B7-L polypeptide multimers.

In general, chemical derivatization may be performed under any suitablecondition used to react a protein with an activated polymer molecule.Methods for preparing chemical derivatives of polypeptides willgenerally comprise the steps of: (a) reacting the polypeptide with theactivated polymer molecule (such as a reactive ester or aldehydederivative of the polymer molecule) under conditions whereby thepolypeptide comprising the amino acid sequence of SEQ ID NO: 2, or otherB7-L polypeptide, becomes attached to one or more polymer molecules, and(b) obtaining the reaction products. The optimal reaction conditionswill be determined based on known parameters and the desired result. Forexample, the larger the ratio of polymer molecules to protein, thegreater the percentage of attached polymer molecule. In one embodiment,the B7-L polypeptide derivative may have a single polymer moleculemoiety at the amino-terminus. See, e.g., U.S. Pat. No. 5,234,784.

The pegylation of a polypeptide may be specifically carried out usingany of the pegylation reactions known in the art. Such reactions aredescribed, for example, in the following references: Francis et al.,1992, Focus on Growth Factors 3:4-10; European Patent Nos. 0154316 and0401384; and U.S. Pat. No. 4,179,337. For example, pegylation may becarried out via an acylation reaction or an alkylation reaction with areactive polyethylene glycol molecule (or an analogous reactivewater-soluble polymer) as described herein. For the acylation reactions,a selected polymer should have a single reactive ester group. Forreductive alkylation, a selected polymer should have a single reactivealdehyde group. A reactive aldehyde is, for example, polyethylene glycolpropionaldehyde, which is water stable, or mono C₁-C₁₀ alkoxy or aryloxyderivatives thereof (see U.S. Pat. No. 5,252,714).

In another embodiment, B7-L polypeptides may be chemically coupled tobiotin. The biotin/B7-L polypeptide molecules are then allowed to bindto avidin, resulting in tetravalent avidin/biotin/B7-L polypeptidemolecules. B7-L polypeptides may also be covalently coupled todinitrophenol (DNP) or trinitrophenol (TNP) and the resulting conjugatesprecipitated with anti-DNP or anti-TNP-IgM to form decameric conjugateswith a valency of 10.

Generally, conditions that may be alleviated or modulated by theadministration of the present B7-L polypeptide derivatives include thosedescribed herein for B7-L polypeptides. However, the B7-L polypeptidederivatives disclosed herein may have additional activities, enhanced orreduced biological activity, or other characteristics, such as increasedor decreased half-life, as compared to the non-derivatized molecules.

Genetically Engineered Non-Human Animals

Additionally included within the scope of the present invention arenon-human animals such as mice, rats, or other rodents; rabbits, goats,sheep, or other farm animals, in which the genes encoding native B7-Lpolypeptide have been disrupted (i.e., “knocked out”) such that thelevel of expression of B7-L polypeptide is significantly decreased orcompletely abolished. Such animals may be prepared using techniques andmethods such as those described in U.S. Pat. No. 5,557,032.

The present invention further includes non-human animals such as mice,rats, or other rodents; rabbits, goats, sheep, or other farm animals, inwhich either the native form of a B7-L gene for that animal or aheterologous B7-L gene is over-expressed by the animal, thereby creatinga “transgenic” animal. Such transgenic animals may be prepared usingwell known methods such as those described in U.S. Pat. No. 5,489,743and International Pub. No. WO 94/28122.

The present invention further includes non-human animals in which thepromoter for one or more of the B7-L polypeptides of the presentinvention is either activated or inactivated (e.g., by using homologousrecombination methods) to alter the level of expression of one or moreof the native B7-L polypeptides.

These non-human animals may be used for drug candidate screening. Insuch screening, the impact of a drug candidate on the animal may bemeasured. For example, drug candidates may decrease or increase theexpression of the B7-L gene. In certain embodiments, the amount of B7-Lpolypeptide that is produced may be measured after the exposure of theanimal to the drug candidate. Additionally, in certain embodiments, onemay detect the actual impact of the drug candidate on the animal. Forexample, over-expression of a particular gene may result in, or beassociated with, a disease or pathological condition. In such cases, onemay test a drug candidate's ability to decrease expression of the geneor its ability to prevent or inhibit a pathological condition. In otherexamples, the production of a particular metabolic product such as afragment of a polypeptide, may result in, or be associated with, adisease or pathological condition. In such cases, one may test a drugcandidate's ability to decrease the production of such a metabolicproduct or its ability to prevent or inhibit a pathological condition.

Assaying for Other Modulators of B7-L Polypeptide Activity

In some situations, it may be desirable to identify molecules that aremodulators, i.e., agonists or antagonists, of the activity of B7-Lpolypeptide. Natural or synthetic molecules that modulate B7-Lpolypeptide may be identified using one or more screening assays, suchas those described herein. Such molecules may be administered either inan ex vivo manner or in an in vivo manner by injection, or by oraldelivery, implantation device, or the like.

“Test molecule” refers to a molecule that is under evaluation for theability to modulate (i.e., increase or decrease) the activity of a B7-Lpolypeptide. Most commonly, a test molecule will interact directly witha B7-L polypeptide. However, it is also contemplated that a testmolecule may also modulate B7-L polypeptide activity indirectly, such asby affecting B7-L gene expression, or by binding to a B7-L polypeptidebinding partner (e.g., receptor or ligand). In one embodiment, a testmolecule will bind to a B7-L polypeptide with an affinity constant of atleast about 10⁻⁶ M, preferably about 10⁻⁸ M, more preferably about 10⁻⁹M, and even more preferably about 10⁻¹⁰ M.

Methods for identifying compounds that interact with B7-L polypeptidesare encompassed by the present invention. In certain embodiments, a B7-Lpolypeptide is incubated with a test molecule under conditions thatpermit the interaction of the test molecule with a B7-L polypeptide, andthe extent of the interaction is measured. The test molecule can bescreened in a substantially purified form or in a crude mixture.

In certain embodiments, a B7-L polypeptide agonist or antagonist may bea protein, peptide, carbohydrate, lipid, or small molecular weightmolecule that interacts with B7-L polypeptide to regulate its activity.Molecules which regulate B7-L polypeptide expression include nucleicacids which are complementary to nucleic acids encoding a B7-Lpolypeptide, or are complementary to nucleic acids sequences whichdirect or control the expression of B7-L polypeptide, and which act asanti-sense regulators of expression.

Once a test molecule has been identified as interacting with a B7-Lpolypeptide, the molecule may be further evaluated for its ability toincrease or decrease B7-L polypeptide activity. The measurement of theinteraction of a test molecule with B7-L polypeptide may be carried outin several formats, including cell-based binding assays, membranebinding assays, solution-phase assays, and immunoassays. In general, atest molecule is incubated with a B7-L polypeptide for a specifiedperiod of time, and B7-L polypeptide activity is determined by one ormore assays for measuring biological activity.

The interaction of test molecules with B7-L polypeptides may also beassayed directly using polyclonal or monoclonal antibodies in animmunoassay. Alternatively, modified forms of B7-L polypeptidescontaining epitope tags as described herein may be used in solution andimmunoassays.

In the event that B7-L polypeptides display biological activity throughan interaction with a binding partner (e.g., a receptor or a ligand), avariety of in vitro assays may be used to measure the binding of a B7-Lpolypeptide to the corresponding binding partner (such as a selectivebinding agent, receptor, or ligand). These assays may be used to screentest molecules for their ability to increase or decrease the rate and/orthe extent of binding of a B7-L polypeptide to its binding partner. Inone assay, a B7-L polypeptide is immobilized in the wells of amicrotiter plate. Radiolabeled B7-L polypeptide binding partner (forexample, iodinated B7-L polypeptide binding partner) and a test moleculecan then be added either one at a time (in either order) orsimultaneously to the wells. After incubation, the wells can be washedand counted for radioactivity, using a scintillation counter, todetermine the extent to which the binding partner bound to the B7-Lpolypeptide. Typically, a molecule will be tested over a range ofconcentrations, and a series of control wells lacking one or moreelements of the test assays can be used for accuracy in the evaluationof the results. An alternative to this method involves reversing the“positions” of the proteins, i.e., immobilizing B7-L polypeptide bindingpartner to the microtiter plate wells, incubating with the test moleculeand radiolabeled B7-L polypeptide, and determining the extent of B7-Lpolypeptide binding. See, e.g., Current Protocols in Molecular Biology,chap. 18 (Ausubel et al., eds., Green Publishers Inc. and Wiley and Sons1995).

As an alternative to radiolabeling, a B7-L polypeptide or its bindingpartner may be conjugated to biotin, and the presence of biotinylatedprotein can then be detected using streptavidin linked to an enzyme,such as horse radish peroxidase (HRP) or alkaline phosphatase (AP),which can be detected colorometrically, or by fluorescent tagging ofstreptavidin. An antibody directed to a B7-L polypeptide or to a B7-Lpolypeptide binding partner, and which is conjugated to biotin, may alsobe used for purposes of detection following incubation of the complexwith enzyme-linked streptavidin linked to AP or HRP.

A B7-L polypeptide or a B7-L polypeptide binding partner can also beimmobilized by attachment to agarose beads, acrylic beads, or othertypes of such inert solid phase substrates. The substrate-proteincomplex can be placed in a solution containing the complementary proteinand the test compound. After incubation, the beads can be precipitatedby centrifugation, and the amount of binding between a B7-L polypeptideand its binding partner can be assessed using the methods describedherein. Alternatively, the substrate-protein complex can be immobilizedin a column with the test molecule and complementary protein passingthrough the column. The formation of a complex between a B7-Lpolypeptide and its binding partner can then be assessed using any ofthe techniques described herein (e.g., radiolabelling or antibodybinding).

Another in vitro assay that is useful for identifying a test moleculethat increases or decreases the formation of a complex between a B7-Lpolypeptide binding protein and a B7-L polypeptide binding partner is asurface plasmon resonance detector system such as the BIAcore assaysystem (Pharmacia, Piscataway, N.J.). The BIAcore system is utilized asspecified by the manufacturer. This assay essentially involves thecovalent binding of either B7-L polypeptide or a B7-L polypeptidebinding partner to a dextran-coated sensor chip that is located in adetector. The test compound and the other complementary protein can thenbe injected, either simultaneously or sequentially, into the chambercontaining the sensor chip. The amount of complementary protein thatbinds can be assessed based on the change in molecular mass that isphysically associated with the dextran-coated side of the sensor chip,with the change in molecular mass being measured by the detector system.

In some cases, it may be desirable to evaluate two or more testcompounds together for their ability to increase or decrease theformation of a complex between a B7-L polypeptide and a B7-L polypeptidebinding partner. In these cases, the assays set forth herein can bereadily modified by adding such additional test compound(s) eithersimultaneously with, or subsequent to, the first test compound. Theremainder of the steps in the assay are as set forth herein.

In vitro assays such as those described herein may be usedadvantageously to screen large numbers of compounds for an effect on theformation of a complex between a B7-L polypeptide and B7-L polypeptidebinding partner. The assays may be automated to screen compoundsgenerated in phage display, synthetic peptide, and chemical synthesislibraries.

Compounds which increase or decrease the formation of a complex betweena B7-L polypeptide and a B7-L polypeptide binding partner may also bescreened in cell culture using cells and cell lines expressing eitherB7-L polypeptide or B7-L polypeptide binding partner. Cells and celllines may be obtained from any mammal, but preferably will be from humanor other primate, canine, or rodent sources. The binding of a B7-Lpolypeptide to cells expressing B7-L polypeptide binding partner at thesurface is evaluated in the presence or absence of test molecules, andthe extent of binding may be determined by, for example, flow cytometryusing a biotinylated antibody to a B7-L polypeptide binding partner.Cell culture assays can be used advantageously to further evaluatecompounds that score positive in protein binding assays describedherein.

Cell cultures can also be used to screen the impact of a drug candidate.For example, drug candidates may decrease or increase the expression ofthe B7-L gene. In certain embodiments, the amount of B7-L polypeptide ora B7-L polypeptide fragment that is produced may be measured afterexposure of the cell culture to the drug candidate. In certainembodiments, one may detect the actual impact of the drug candidate onthe cell culture. For example, the over-expression of a particular genemay have a particular impact on the cell culture. In such cases, one maytest a drug candidate's ability to increase or decrease the expressionof the gene or its ability to prevent or inhibit a particular impact onthe cell culture. In other examples, the production of a particularmetabolic product such as a fragment of a polypeptide, may result in, orbe associated with, a disease or pathological condition. In such cases,one may test a drug candidate's ability to decrease the production ofsuch a metabolic product in a cell culture.

Internalizing Proteins

The tat protein sequence (from HIV) can be used to internalize proteinsinto a cell. See, e.g., Falwell et al., 1994, Proc. Natl. Acad. Sci.U.S.A. 91:664-68. For example, an 11 amino acid sequence(Y-G-R-K-K-R-R-Q-R-R-R; SEQ ID NO: 24) of the HIV tat protein (termedthe “protein transduction domain,” or TAT PDT) has been described asmediating delivery across the cytoplasmic membrane and the nuclearmembrane of a cell. See Schwarze et al., 1999, Science 285:1569-72; andNagahara et al., 1998, Nat. Med. 4:1449-52. In these procedures,FITC-constructs (FITC-labeled G-G-G-G-Y-G-R-K-K-R-R-Q-R-R-R SEQ ID NO:25), which penetrate tissues following intraperitoneal administration,are prepared, and the binding of such constructs to cells is detected byfluorescence-activated cell sorting (FACS) analysis. Cells treated witha tat-β-gal fusion protein will demonstrate p-gal activity. Followinginjection, expression of such a construct can be detected in a number oftissues, including liver, kidney, lung, heart, and brain tissue. It isbelieved that such constructs undergo some degree of unfolding in orderto enter the cell, and as such, may require a refolding following entryinto the cell.

It will thus be appreciated that the tat protein sequence may be used tointernalize a desired polypeptide into a cell. For example, using thetat protein sequence, a B7-L antagonist (such as an anti-B7-L selectivebinding agent, small molecule, soluble receptor, or antisenseoligonucleotide) can be administered intracellularly to inhibit theactivity of a B7-L molecule. As used herein, the term “B7-L molecule”refers to both B7-L nucleic acid molecules and B7-L polypeptides asdefined herein. Where desired, the B7-L protein itself may also beinternally administered to a cell using these procedures. See also,Straus, 1999, Science 285:1466-67.

Cell Source Identification Using B7-L Polypeptide

In accordance with certain embodiments of the invention, it may beuseful to be able to determine the source of a certain cell typeassociated with a B7-L polypeptide. For example, it may be useful todetermine the origin of a disease or pathological condition as an aid inselecting an appropriate therapy. In certain embodiments, nucleic acidsencoding a B7-L polypeptide can be used as a probe to identify cellsdescribed herein by screening the nucleic acids of the cells with such aprobe. In other embodiments, one may use anti-B7-L polypeptideantibodies to test for the presence of B7-L polypeptide in cells, andthus, determine if such cells are of the types described herein.

B7-L Polypeptide Compositions and Administration

Therapeutic compositions are within the scope of the present invention.Such B7-L polypeptide pharmaceutical compositions may comprise atherapeutically effective amount of a B7-L polypeptide or a B7-L nucleicacid molecule in admixture with a pharmaceutically or physiologicallyacceptable formulation agent selected for suitability with the mode ofadministration. Pharmaceutical compositions may comprise atherapeutically effective amount of one or more B7-L polypeptideselective binding agents in admixture with a pharmaceutically orphysiologically acceptable formulation agent selected for suitabilitywith the mode of administration.

Acceptable formulation materials preferably are nontoxic to recipientsat the dosages and concentrations employed.

The pharmaceutical composition may contain formulation materials formodifying, maintaining, or preserving, for example, the pH, osmolarity,viscosity, clarity, color, isotonicity, odor, sterility, stability, rateof dissolution or release, adsorption, or penetration of thecomposition. Suitable formulation materials include, but are not limitedto, amino acids (such as glycine, glutamine, asparagine, arginine, orlysine), antimicrobials, antioxidants (such as ascorbic acid, sodiumsulfite, or sodium hydrogen-sulfite), buffers (such as borate,bicarbonate, Tris-HCl, citrates, phosphates, or other organic acids),bulking agents (such as mannitol or glycine), chelating agents (such asethylenediamine tetraacetic acid (EDTA)), complexing agents (such ascaffeine, polyvinylpyrrolidone, beta-cyclodextrin, orhydroxypropyl-beta-cyclodextrin), fillers, monosaccharides,disaccharides, and other carbohydrates (such as glucose, mannose, ordextrins), proteins (such as serum albumin, gelatin, orimmunoglobulins), coloring, flavoring and diluting agents, emulsifyingagents, hydrophilic polymers (such as polyvinylpyrrolidone), lowmolecular weight polypeptides, salt-forming counterions (such assodium), preservatives (such as benzalkonium chloride, benzoic acid,salicylic acid, thimerosal, phenethyl alcohol, methylparaben,propylparaben, chlorhexidine, sorbic acid, or hydrogen peroxide),solvents (such as glycerin, propylene glycol, or polyethylene glycol),sugar alcohols (such as mannitol or sorbitol), suspending agents,surfactants or wetting agents (such as pluronics; PEG; sorbitan esters;polysorbates such as polysorbate 20 or polysorbate 80; triton;tromethamine; lecithin; cholesterol or tyloxapal), stability enhancingagents (such as sucrose or sorbitol), tonicity enhancing agents (such asalkali metal halides—preferably sodium or potassium chloride—or mannitolsorbitol), delivery vehicles, diluents, excipients and/or pharmaceuticaladjuvants. See Remington's Pharmaceutical Sciences (18th Ed., A. R.Gennaro, ed., Mack Publishing Company 1990.

The optimal pharmaceutical composition will be determined by a skilledartisan depending upon, for example, the intended-route ofadministration, delivery format, and desired dosage. See, e.g.,Remington's Pharmaceutical Sciences, supra. Such compositions mayinfluence the physical state, stability, rate of in vivo release, andrate of in vivo clearance of the B7-L molecule.

The primary vehicle or carrier in a pharmaceutical composition may beeither aqueous or non-aqueous in nature. For example, a suitable vehicleor carrier for injection may be water, physiological saline solution, orartificial cerebrospinal fluid, possibly supplemented with othermaterials common in compositions for parenteral administration. Neutralbuffered saline or saline mixed with serum albumin are further exemplaryvehicles. Other exemplary pharmaceutical compositions comprise Trisbuffer of about pH 7.0-8.5, or acetate buffer of about pH 4.0-5.5, whichmay further include sorbitol or a suitable substitute. In one embodimentof the present invention, B7-L polypeptide compositions may be preparedfor storage by mixing the selected composition having the desired degreeof purity with optional formulation agents (Remington's PharmaceuticalSciences, supra) in the form of a lyophilized cake or an aqueoussolution. Further, the B7-L polypeptide product may be formulated as alyophilizate using appropriate excipients such as sucrose.

The B7-L polypeptide pharmaceutical compositions can be selected forparenteral delivery. Alternatively, the compositions may be selected forinhalation or for delivery through the digestive tract, such as orally.The preparation of such pharmaceutically acceptable compositions iswithin the skill of the art.

The formulation components are present in concentrations that areacceptable to the site of administration. For example, buffers are usedto maintain the composition at physiological pH or at a slightly lowerpH, typically within a pH range of from about 5 to about 8.

When parenteral administration is contemplated, the therapeuticcompositions for use in this invention may be in the form of apyrogen-free, parenterally acceptable, aqueous solution comprising thedesired B7-L molecule in a pharmaceutically acceptable vehicle. Aparticularly suitable vehicle for parenteral injection is steriledistilled water in which a B7-L molecule is formulated as a sterile,isotonic solution, properly preserved. Yet another preparation caninvolve the formulation of the desired molecule with an agent, such asinjectable microspheres, bio-erodible particles, polymeric compounds(such as polylactic acid or polyglycolic acid), beads, or liposomes,that provides for the controlled or sustained release of the productwhich may then be delivered via a depot injection. Hyaluronic acid mayalso be used, and this may have the effect of promoting sustainedduration in the circulation. Other suitable means for the introductionof the desired molecule include implantable drug delivery devices.

In one embodiment, a pharmaceutical composition may be formulated forinhalation. For example, B7-L polypeptide may be formulated as a drypowder for inhalation. B7-L polypeptide or nucleic acid moleculeinhalation solutions may also be formulated with a propellant foraerosol delivery. In yet another embodiment, solutions may be nebulized.Pulmonary administration is further described in International Pub. No.WO 94/20069, which describes the pulmonary delivery of chemicallymodified proteins.

It is also contemplated that certain formulations may be administeredorally. In one embodiment of the present invention, B7-L polypeptidesthat are administered in this fashion can be formulated with or withoutthose carriers customarily used in the compounding of solid dosage formssuch as tablets and capsules. For example, a capsule may be designed torelease the active portion of the formulation at the point in thegastrointestinal tract when bioavailability is maximized andpre-systemic degradation is minimized. Additional agents can be includedto facilitate absorption of the B7-L polypeptide. Diluents, flavorings,low melting point waxes, vegetable oils, lubricants, suspending agents,tablet disintegrating agents, and binders may also be employed.

Another pharmaceutical composition may involve an effective quantity ofB7-L polypeptides in a mixture with non-toxic excipients that aresuitable for the manufacture of tablets. By dissolving the tablets insterile water, or another appropriate vehicle, solutions can be preparedin unit-dose form. Suitable excipients include, but are not limited to,inert diluents, such as calcium carbonate, sodium carbonate orbicarbonate, lactose, or calcium phosphate; or binding agents, such asstarch, gelatin, or acacia; or lubricating agents such as magnesiumstearate, stearic acid, or talc.

Additional B7-L polypeptide pharmaceutical compositions will be evidentto those skilled in the art, including formulations involving B7-Lpolypeptides in sustained- or controlled-delivery formulations.Techniques for formulating a variety of other sustained- orcontrolled-delivery means, such as liposome carriers, bio-erodiblemicroparticles or porous beads and depot injections, are also known tothose skilled in the art. See, e.g., International App. No.PCT/US93/00829, which describes the controlled release of porouspolymeric microparticles for the delivery of pharmaceuticalcompositions.

Additional examples of sustained-release preparations includesemipermeable polymer matrices in the form of shaped articles, e.g.films, or microcapsules. Sustained release matrices may includepolyesters, hydrogels, polylactides (U.S. Pat. No. 3,773,919 andEuropean Patent No. 058481), copolymers of L-glutamic acid and gammaethyl-L-glutamate (Sidman et al., 1983, Biopolymers 22:547-56),poly(2-hydroxyethyl-methacrylate) (Langer et al., 1981, J. Biomed.Mater. Res. 15:167-277 and Langer, 1982, Chem. Tech. 12:98-105),ethylene vinyl acetate (Langer et al., supra) orpoly-D(−)-3-hydroxybutyric acid (European Patent No. 133988).Sustained-release compositions may also include liposomes, which can beprepared by any of several methods known in the art. See, e.g., Eppsteinet al., 1985, Proc. Natl. Acad. Sci. USA 82:3688-92; and European PatentNos. 036676, 088046, and 143949.

The B7-L pharmaceutical composition to be used for in vivoadministration typically must be sterile. This may be accomplished byfiltration through sterile filtration membranes. Where the compositionis lyophilized, sterilization using this method may be conducted eitherprior to, or following, lyophilization and reconstitution. Thecomposition for parenteral administration may be stored in lyophilizedform or in a solution. In addition, parenteral compositions generallyare placed into a container having a sterile access port, for example,an intravenous solution bag or vial having a stopper pierceable by ahypodermic injection needle.

Once the pharmaceutical composition has been formulated, it may bestored in sterile vials as a solution, suspension, gel, emulsion, solid,or as a dehydrated or lyophilized powder. Such formulations may bestored either in a ready-to-use form or in a form (e.g., lyophilized)requiring reconstitution prior to administration.

In a specific embodiment, the present invention is directed to kits forproducing a single-dose administration unit. The kits may each containboth a first container having a dried protein and a second containerhaving an aqueous formulation. Also included within the scope of thisinvention are kits containing single and multi-chambered pre-filledsyringes (e.g., liquid syringes and lyosyringes).

The effective amount of a B7-L pharmaceutical composition to be employedtherapeutically will depend, for example, upon the therapeutic contextand objectives. One skilled in the art will appreciate that theappropriate dosage levels for treatment will thus vary depending, inpart, upon the molecule delivered, the indication for which the B7-Lmolecule is being used, the route of administration, and the size (bodyweight, body surface, or organ size) and condition (the age and generalhealth) of the patient. Accordingly, the clinician may titer the dosageand modify the route of administration to obtain the optimal therapeuticeffect. A typical dosage may range from about 0.1 μg/kg to up to about100 mg/kg or more, depending on the factors mentioned above. In otherembodiments, the dosage may range from 0.1 μg/kg up to about 100 mg/kg;or 1 μg/kg up to about 100 mg/kg; or 5 μg/kg up to about 100 mg/kg.

The frequency of dosing will depend upon the pharmacokinetic parametersof the B7-L molecule in the formulation being used. Typically, aclinician will administer the composition until a dosage is reached thatachieves the desired effect. The composition may therefore beadministered as a single dose, as two or more doses (which may or maynot contain the same amount of the desired molecule) over time, or as acontinuous infusion via an implantation device or catheter. Furtherrefinement of the appropriate dosage is routinely made by those ofordinary skill in the art and is within the ambit of tasks routinelyperformed by them. Appropriate dosages may be ascertained through use ofappropriate dose-response data.

The route of administration of the pharmaceutical composition is inaccord with known methods, e.g., orally; through injection byintravenous, intraperitoneal, intracerebral (intraparenchymal),intracerebroventricular, intramuscular, intraocular, intraarterial,intraportal, or intralesional routes; by sustained release systems; orby implantation devices. Where desired, the compositions may beadministered by bolus injection or continuously by infusion, or byimplantation device.

Alternatively or additionally, the composition may be administeredlocally via implantation of a membrane, sponge, or other appropriatematerial onto which the desired molecule has been absorbed orencapsulated. Where an implantation device is used, the device may beimplanted into any suitable tissue or organ, and delivery of the desiredmolecule may be via diffusion, timed-release bolus, or continuousadministration.

In some cases, it may be desirable to use B7-L polypeptidepharmaceutical compositions in an ex vivo manner. In such instances,cells, tissues, or organs that have been removed from the patient areexposed to B7-L polypeptide pharmaceutical compositions after which thecells, tissues, or organs are subsequently implanted back into thepatient.

In other cases, a B7-L polypeptide can be delivered by implantingcertain cells that have been genetically engineered, using methods suchas those described herein, to express and secrete the B7-L polypeptide.Such cells may be animal or human cells, and may be autologous,heterologous, or xenogeneic. Optionally, the cells may be immortalized.In order to decrease the chance of an immunological response, the cellsmay be encapsulated to avoid infiltration of surrounding tissues. Theencapsulation materials are typically biocompatible, semi-permeablepolymeric enclosures or membranes that allow the release of the proteinproduct(s) but prevent the destruction of the cells by the patient'simmune system or by other detrimental factors from the surroundingtissues.

As discussed herein, it may be desirable to treat isolated cellpopulations (such as stem cells, lymphocytes, red blood cells,chondrocytes, neurons, and the like) with one or more B7-L polypeptides.This can be accomplished by exposing the isolated cells to thepolypeptide directly, where it is in a form that is permeable to thecell membrane.

Additional embodiments of the present invention relate to cells andmethods (e.g., homologous recombination and/or other recombinantproduction methods) for both the in vitro production of therapeuticpolypeptides and for the production and delivery of therapeuticpolypeptides by gene therapy or cell therapy. Homologous and otherrecombination methods may be used to modify a cell that contains anormally transcriptionally-silent B7-L gene, or an under-expressed gene,and thereby produce a cell which expresses therapeutically efficaciousamounts of B7-L polypeptides.

Homologous recombination is a technique originally developed fortargeting genes to induce or correct mutations in transcriptionallyactive genes. Kucherlapati, 1989, Prog. in Nucl. Acid Res. & Mol. Biol.36:301. The basic technique was developed as a method for introducingspecific mutations into specific regions of the mammalian genome (Thomaset al., 1986, Cell 44:419-28; Thomas and Capecchi, 1987, Cell 51:503-12;Doetschman et al., 1988, Proc. Natl. Acad. Sci. U.S.A. 85:8583-87) or tocorrect specific mutations within defective genes (Doetschman et al.,1987, Nature 330:576-78). Exemplary homologous recombination techniquesare described in U.S. Pat. No. 5,272,071; European Patent Nos. 9193051and 505500; International App. No. PCT/US90/07642, and International PubNo. WO 91/09955).

Through homologous recombination, the DNA sequence to be inserted intothe genome can be directed to a specific region of the gene of interestby attaching it to targeting DNA. The targeting DNA is a nucleotidesequence that is complementary (homologous) to a region of the genomicDNA. Small pieces of targeting DNA that are complementary to a specificregion of the genome are put in contact with the parental strand duringthe DNA replication process. It is a general property of DNA that hasbeen inserted into a cell to hybridize, and therefore, recombine withother pieces of endogenous DNA through shared homologous regions. Ifthis complementary strand is attached to an oligonucleotide thatcontains a mutation or a different sequence or an additional nucleotide,it too is incorporated into the newly synthesized strand as a result ofthe recombination. As a result of the proofreading function, it ispossible for the new sequence of DNA to serve as the template. Thus, thetransferred DNA is incorporated into the genome.

Attached to these pieces of targeting DNA are regions of DNA that mayinteract with or control the expression of a B7-L polypeptide, e.g.,flanking sequences. For example, a promoter/enhancer element, asuppressor, or an exogenous transcription modulatory element is insertedin the genome of the intended host cell in proximity and orientationsufficient to influence the transcription of DNA encoding the desiredB7-L polypeptide. The control element controls a portion of the DNApresent in the host cell genome. Thus, the expression of the desiredB7-L polypeptide may be achieved not by transfection of DNA that encodesthe B7-L gene itself, but rather by the use of targeting DNA (containingregions of homology with the endogenous gene of interest) coupled withDNA regulatory segments that provide the endogenous gene sequence withrecognizable signals for transcription of a B7-L gene.

In an exemplary method, the expression of a desired targeted gene in acell (i.e., a desired endogenous cellular gene) is altered viahomologous recombination into the cellular genome at a preselected site,by the introduction of DNA that includes at least a regulatory sequence,an exon, and a splice donor site. These components are introduced intothe chromosomal (genomic) DNA in such a manner that this, in effect,results in the production of a new transcription unit (in which theregulatory sequence, the exon, and the splice donor site present in theDNA construct are operatively linked to the endogenous gene). As aresult of the introduction of these components into the chromosomal DNA,the expression of the desired endogenous gene is altered.

Altered gene expression, as described herein, encompasses activating (orcausing to be expressed) a gene which is normally silent (unexpressed)in the cell as obtained, as well as increasing the expression of a genewhich is not expressed at physiologically significant levels in the cellas obtained. The embodiments further encompass changing the pattern ofregulation or induction such that it is different from the pattern ofregulation or induction that occurs in the cell as obtained, andreducing (including eliminating) the expression of a gene which isexpressed in the cell as obtained.

One method by which homologous recombination can be used to increase, orcause, B7-L polypeptide production from a cell's endogenous B7-L geneinvolves first using homologous recombination to place a recombinationsequence from a site-specific recombination system (e.g., Cre/loxP,FLP/FRT) (Sauer, 1994, Curr. Opin. Biotechnol., 5:521-27; Sauer, 1993,Methods Enzymol., 225:890-900) upstream of (i.e., 5′ to) the cell'sendogenous genomic B7-L polypeptide coding region. A plasmid containinga recombination site homologous to the site that was placed justupstream of the genomic B7-L polypeptide coding region is introducedinto the modified cell line along with the appropriate recombinaseenzyme. This recombinase causes the plasmid to integrate, via theplasmid's recombination site, into the recombination site located justupstream of the genomic B7-L polypeptide coding region in the cell line(Baubonis and Sauer, 1993, Nucleic Acids Res. 21:2025-29; O'Gorman etal., 1991, Science 251:1351-55). Any flanking sequences known toincrease transcription (e.g., enhancer/promoter, intron, translationalenhancer), if properly positioned in this plasmid, would integrate insuch a manner as to create a new or modified transcriptional unitresulting in de novo or increased B7-L polypeptide production from thecell's endogenous B7-L gene.

A further method to use the cell line in which the site specificrecombination sequence had been placed just upstream of the cell'sendogenous genomic B7-L polypeptide coding region is to use homologousrecombination to introduce a second recombination site elsewhere in thecell line's genome. The appropriate recombinase enzyme is thenintroduced into the two-recombination-site cell line, causing arecombination event (deletion, inversion, and translocation) (Sauer,1994, Curr. Opin. Biotechnol., 5:521-27; Sauer, 1993, Methods Enzymol.,225:890-900) that would create a new or modified transcriptional unitresulting in de novo or increased B7-L polypeptide production from thecell's endogenous B7-L gene.

An additional approach for increasing, or causing, the expression ofB7-L polypeptide from a cell's endogenous B7-L gene involves increasing,or causing, the expression of a gene or genes (e.g., transcriptionfactors) and/or decreasing the expression of a gene or genes (e.g.,transcriptional repressors) in a manner which results in de novo orincreased B7-L polypeptide production from the cell's endogenous B7-Lgene. This method includes the introduction of a non-naturally occurringpolypeptide (e.g., a polypeptide comprising a site specific DNA bindingdomain fused to a transcriptional factor domain) into the cell such thatde novo or increased B7-L polypeptide production from the cell'sendogenous B7-L gene results.

The present invention further relates to DNA constructs useful in themethod of altering expression of a target gene. In certain embodiments,the exemplary DNA constructs comprise: (a) one or more targetingsequences, (b) a regulatory sequence, (c) an exon, and (d) an unpairedsplice-donor site. The targeting sequence in the DNA construct directsthe integration of elements (a)-(d) into a target gene in a cell suchthat the elements (b)-(d) are operatively linked to sequences of theendogenous target gene. In another embodiment, the DNA constructscomprise: (a) one or more targeting sequences, (b) a regulatorysequence, (c) an exon, (d) a splice-donor site, (e) an intron, and (f) asplice-acceptor site, wherein the targeting sequence directs theintegration of elements (a)-(f) such that the elements of (b)-(f) areoperatively linked to the endogenous gene. The targeting sequence ishomologous to the preselected site in the cellular chromosomal DNA withwhich homologous recombination is to occur. In the construct, the exonis generally 3′ of the regulatory sequence and the splice-donor site is3′ of the exon.

If the sequence of a particular gene is known, such as the nucleic acidsequence of B7-L polypeptide presented herein, a piece of DNA that iscomplementary to a selected region of the gene can be synthesized orotherwise obtained, such as by appropriate restriction of the native DNAat specific recognition sites bounding the region of interest. Thispiece serves as a targeting sequence upon insertion into the cell andwill hybridize to its homologous region within the genome. If thishybridization occurs during DNA replication, this piece of DNA, and anyadditional sequence attached thereto, will act as an Okazaki fragmentand will be incorporated into the newly synthesized daughter strand ofDNA. The present invention, therefore, includes nucleotides encoding aB7-L polypeptide, which nucleotides may be used as targeting sequences.

B7-L polypeptide cell therapy, e.g., the implantation of cells producingB7-L polypeptides, is also contemplated. This embodiment involvesimplanting cells capable of synthesizing and secreting a biologicallyactive form of B7-L polypeptide. Such B7-L polypeptide-producing cellscan be cells that are natural producers of B7-L polypeptides or may berecombinant cells whose ability to produce B7-L polypeptides has beenaugmented by transformation with a gene encoding the desired B7-Lpolypeptide or with a gene augmenting the expression of B7-Lpolypeptide. Such a modification may be accomplished by means of avector suitable for delivering the gene as well as promoting itsexpression and secretion. In order to minimize a potential immunologicalreaction in patients being administered a B7-L polypeptide, as may occurwith the administration of a polypeptide of a foreign species, it ispreferred that the natural cells producing B7-L polypeptide be of humanorigin and produce human B7-L polypeptide. Likewise, it is preferredthat the recombinant cells producing B7-L polypeptide be transformedwith an expression vector containing a gene encoding a human B7-Lpolypeptide.

Implanted cells may be encapsulated to avoid the infiltration ofsurrounding tissue. Human or non-human animal cells may be implanted inpatients in biocompatible, semipermeable polymeric enclosures ormembranes that allow the release of B7-L polypeptide, but that preventthe destruction of the cells by the patient's immune system or by otherdetrimental factors from the surrounding tissue. Alternatively, thepatient's own cells, transformed to produce B7-L polypeptides ex vivo,may be implanted directly into the patient without such encapsulation.

Techniques for the encapsulation of living cells are known in the art,and the preparation of the encapsulated cells and their implantation inpatients may be routinely accomplished. For example, Baetge et al.(International Pub. No. WO 95/05452 and International App. No.PCT/US94/09299) describe membrane capsules containing geneticallyengineered cells for the effective delivery of biologically activemolecules. The capsules are biocompatible and are easily retrievable.The capsules encapsulate cells transfected with recombinant DNAmolecules comprising DNA sequences coding for biologically activemolecules operatively linked to promoters that are not subject todown-regulation in vivo upon implantation into a mammalian host. Thedevices provide for the delivery of the molecules from living cells tospecific sites within a recipient. In addition, see U.S. Pat. Nos.4,892,538; 5,011,472; and 5,106,627. A system for encapsulating livingcells is described in International Pub. No. WO 91/10425 (Aebischer etal.). See also, International Pub. No. WO 91/10470 (Aebischer et al.);Winn et al., 1991, Exper. Neurol. 113:322-29; Aebischer et al., 1991,Exper. Neurol. 111:269-75; and Tresco et al., 1992, ASAIO 38:17-23.

In vivo and in vitro gene therapy delivery of B7-L polypeptides is alsoenvisioned. One example of a gene therapy technique is to use the B7-Lgene (either genomic DNA, cDNA, and/or synthetic DNA) encoding a B7-Lpolypeptide that may be operably linked to a constitutive or induciblepromoter to form a “gene therapy DNA construct.” The promoter may behomologous or heterologous to the endogenous B7-L gene, provided that itis active in the cell or tissue type into which the construct will beinserted. Other components of the gene therapy DNA construct mayoptionally include DNA molecules designed for site-specific integration(e.g., endogenous sequences useful for homologous recombination),tissue-specific promoters, enhancers or silencers, DNA molecules capableof providing a selective advantage over the parent cell, DNA moleculesuseful as labels to identify transformed cells, negative selectionsystems, cell specific binding agents (as, for example, for celltargeting), cell-specific internalization factors, transcription factorsenhancing expression from a vector, and factors enabling vectorproduction.

A gene therapy DNA construct can then be introduced into cells (eitherex vivo or in vivo) using viral or non-viral vectors. One means forintroducing the gene therapy DNA construct is by means of viral vectorsas described herein. Certain vectors, such as retroviral vectors, willdeliver the DNA construct to the chromosomal DNA of the cells, and thegene can integrate into the chromosomal DNA. Other vectors will functionas episomes, and the gene therapy DNA construct will remain in thecytoplasm.

In yet other embodiments, regulatory elements can be included for thecontrolled expression of the B7-L gene in the target cell. Such elementsare turned on in response to an appropriate effector. In this way, atherapeutic polypeptide can be expressed when desired. One conventionalcontrol means involves the use of small molecule dimerizers or rapalogsto dimerize chimeric proteins which contain a small molecule-bindingdomain and a domain capable of initiating a biological process, such asa DNA-binding protein or transcriptional activation protein (seeInternational Pub. Nos. WO 96/41865, WO 97/31898, and WO 97/31899). Thedimerization of the proteins can be used to initiate transcription ofthe transgene.

An alternative regulation technology uses a method of storing proteinsexpressed from the gene of interest inside the cell as an aggregate orcluster. The gene of interest is expressed as a fusion protein thatincludes a conditional aggregation domain that results in the retentionof the aggregated protein in the endoplasmic reticulum. The storedproteins are stable and inactive inside the cell. The proteins can bereleased, however, by administering a drug (e.g., small molecule ligand)that removes the conditional aggregation domain and thereby specificallybreaks apart the aggregates or clusters so that the proteins may besecreted from the cell. See Aridor et al, 2000, Science 287:816-17 andRivera et al., 2000, Science 287:826-30.

Other suitable control means or gene switches include, but are notlimited to, the systems described herein. Mifepristone (RU486) is usedas a progesterone antagonist. The binding of a modified progesteronereceptor ligand-binding domain to the progesterone antagonist activatestranscription by forming a dimer of two transcription factors that thenpass into the nucleus to bind DNA. The ligand-binding domain is modifiedto eliminate the ability of the receptor to bind to the natural ligand.The modified steroid hormone receptor system is further described inU.S. Pat. No. 5,364,791 and International Pub. Nos. WO 96/40911 and WO97/10337.

Yet another control system uses ecdysone (a fruit fly steroid hormone),which binds to and activates an ecdysone receptor (cytoplasmicreceptor). The receptor then translocates to the nucleus to bind aspecific DNA response element (promoter from ecdysone-responsive gene).The ecdysone receptor includes a transactivation domain, DNA-bindingdomain, and ligand-binding domain to initiate transcription. Theecdysone system is further described in U.S. Pat. No. 5,514,578 andInternational Pub. Nos. WO 97/38117, WO 96/37609, and WO 93/03162.

Another control means uses a positive tetracycline-controllabletransactivator. This system involves a mutated tet repressor proteinDNA-binding domain (mutated tet R-4 amino acid changes which resulted ina reverse tetracycline-regulated transactivator protein, i.e., it bindsto a tet operator in the presence of tetracycline) linked to apolypeptide which activates transcription. Such systems are described inU.S. Pat. Nos. 5,464,758, 5,650,298, and 5,654,168.

Additional expression control systems and nucleic acid constructs aredescribed in U.S. Pat. Nos. 5,741,679 and 5,834,186, to InnovirLaboratories Inc.

In vivo gene therapy may be accomplished by introducing the geneencoding B7-L polypeptide into cells via local injection of a B7-Lnucleic acid molecule or by other appropriate viral or non-viraldelivery vectors. Hefti 1994, Neurobiology 25:1418-35. For example, anucleic acid molecule encoding a B7-L polypeptide may be contained in anadeno-associated virus (AAV) vector for delivery to the targeted cells(see, e.g., Johnson, International Pub. No. WO 95/34670; InternationalApp. No. PCT/US95/07178). The recombinant AAV genome typically containsAAV inverted terminal repeats flanking a DNA sequence encoding a B7-Lpolypeptide operably linked to functional promoter and polyadenylationsequences.

Alternative suitable viral vectors include, but are not limited to,retrovirus, adenovirus, herpes simplex virus, lentivirus, hepatitisvirus, parvovirus, papovavirus, poxvirus, alphavirus, coronavirus,rhabdovirus, paramyxovirus, and papilloma virus vectors. U.S. Pat. No.5,672,344 describes an in vivo viral-mediated gene transfer systeminvolving a recombinant neurotrophic HSV-1 vector. U.S. Pat. No.5,399,346 provides examples of a process for providing a patient with atherapeutic protein by the delivery of human cells that have beentreated in vitro to insert a DNA segment encoding a therapeutic protein.Additional methods and materials for the practice of gene therapytechniques are described in U.S. Pat. Nos. 5,631,236 (involvingadenoviral vectors), 5,672,510 (involving retroviral vectors), 5,635,399(involving retroviral vectors expressing cytokines).

Nonviral delivery methods include, but are not limited to,liposome-mediated transfer, naked DNA delivery (direct injection),receptor-mediated transfer (ligand-DNA complex), electroporation,calcium phosphate precipitation, and microparticle bombardment (e.g.,gene gun). Gene therapy materials and methods may also include induciblepromoters, tissue-specific enhancer-promoters, DNA sequences designedfor site-specific integration, DNA sequences capable of providing aselective advantage over the parent cell, labels to identify transformedcells, negative selection systems and expression control systems (safetymeasures), cell-specific binding agents (for cell targeting),cell-specific internalization factors, and transcription factors toenhance expression by a vector as well as methods of vector manufacture.Such additional methods and materials for the practice of gene therapytechniques are described in U.S. Pat. Nos. 4,970,154 (involvingelectroporation techniques), 5,679,559 (describing alipoprotein-containing system for gene delivery), 5,676,954 (involvingliposome carriers), 5,593,875 (describing methods for calcium phosphatetransfection), and 4,945,050 (describing a process wherein biologicallyactive particles are propelled at cells at a speed whereby the particlespenetrate the surface of the cells and become incorporated into theinterior of the cells), and International Pub. No. WO 96/40958(involving nuclear ligands).

It is also contemplated that B7-L gene therapy or cell therapy canfurther include the delivery of one or more additional polypeptide(s) inthe same or a different cell(s). Such cells may be separately introducedinto the patient, or the cells may be contained in a single implantabledevice, such as the encapsulating membrane described above, or the cellsmay be separately modified by means of viral vectors.

A means to increase endogenous B7-L polypeptide expression in a cell viagene therapy is to insert one or more enhancer elements into the B7-Lpolypeptide promoter, where the enhancer elements can serve to increasetranscriptional activity of the B7-L gene. The enhancer elements usedwill be selected based on the tissue in which one desires to activatethe gene—enhancer elements known to confer promoter activation in thattissue will be selected. For example, if a gene encoding a B7-Lpolypeptide is to be “turned on” in T-cells, the lck promoter enhancerelement may be used. Here, the functional portion of the transcriptionalelement to be added may be inserted into a fragment of DNA containingthe B7-L polypeptide promoter (and optionally, inserted into a vectorand/or 5′ and/or 3′ flanking sequences) using standard cloningtechniques. This construct, known as a “homologous recombinationconstruct,” can then be introduced into the desired cells either ex vivoor in vivo.

Gene therapy also can be used to decrease B7-L polypeptide expression bymodifying the nucleotide sequence of the endogenous promoter. Suchmodification is typically accomplished via homologous recombinationmethods. For example, a DNA molecule containing all or a portion of thepromoter of the B7-L gene selected for inactivation can be engineered toremove and/or replace pieces of the promoter that regulatetranscription. For example, the TATA box and/or the binding site of atranscriptional activator of the promoter may be deleted using standardmolecular biology techniques; such deletion can inhibit promoteractivity thereby repressing the transcription of the corresponding B7-Lgene. The deletion of the TATA box or the transcription activatorbinding site in the promoter may be accomplished by generating a DNAconstruct comprising all or the relevant portion of the B7-L polypeptidepromoter (from the same or a related species as the B7-L gene to beregulated) in which one or more of the TATA box and/or transcriptionalactivator binding site nucleotides are mutated via substitution,deletion and/or insertion of one or more nucleotides. As a result, theTATA box and/or activator binding site has decreased activity or isrendered completely inactive. This construct, which also will typicallycontain at least about 500 bases of DNA that correspond to the native(endogenous) 5′ and 3′ DNA sequences adjacent to the promoter segmentthat has been modified, may be introduced into the appropriate cells(either ex vivo or in vivo) either directly or via a viral vector asdescribed herein. Typically, the integration of the construct into thegenomic DNA of the cells will be via homologous recombination, where the5′ and 3′ DNA sequences in the promoter construct can serve to helpintegrate the modified promoter region via hybridization to theendogenous chromosomal DNA.

Therapeutic Uses

B7-L nucleic acid molecules, polypeptides, and agonists and antagoniststhereof can be used to treat, diagnose, ameliorate, or prevent a numberof diseases, disorders, or conditions, including those recited herein.

B7-L polypeptide agonists and antagonists include those molecules whichregulate B7-L polypeptide activity and either increase or decrease atleast one activity of the mature form of the B7-L polypeptide. Agonistsor antagonists may be co-factors, such as a protein, peptide,carbohydrate, lipid, or small molecular weight molecule, which interactwith B7-L polypeptide and thereby regulate its activity. Potentialpolypeptide agonists or antagonists include antibodies that react witheither soluble or membrane-bound forms of B7-L polypeptides thatcomprise part or all of the extracellular domains of the said proteins.Molecules that regulate B7-L polypeptide expression typically includenucleic acids encoding B7-L polypeptide that can act as anti-senseregulators of expression.

Since transgenic mice expressing a related member of the B7 familyshowed seminal vesicle hyperplasia (co-pending U.S. patent applicationSer. No. 09/729,264, filed Nov. 28, 2000), B7-L polypeptide agonists andantagonists may be useful in the treatment of reproductive disorders andproliferative disorders.

The overexpression of B7-L polypeptide may play a role in the growth andmaintenance of cancer cells by causing seminal vesicle hyperplasia.Accordingly, agonists or antagonists to B7-L polypeptide may be usefulfor the diagnosis or treatment of cancer. Examples of such cancersinclude, but are not limited to, seminal vesicle cancer, lung cancer,brain cancer, breast cancer, cancers of the hematopoietic system,prostate cancer, ovarian cancer, and testicular cancer. Other cancersare encompassed within the scope of the invention.

The overexpression of B7-L polypeptide may play a role in theinappropriate proliferation of cells by causing seminal vesiclehyperplasia. B7-L polypeptide may play a role in the inappropriateproliferation of cells based on overexpression causing seminal vesiclehyperplasia. Accordingly, agonists or antagonists to B7-L polypeptidemay be useful for the diagnosis or treatment of diseases associated withabnormal cell proliferation. Examples of such diseases include, but arenot limited to, arteriosclerosis and vascular restenosis. Other diseasesinfluenced by the inappropriate proliferation of cells are encompassedwithin the scope of the invention.

The overexpression of B7-L polypeptide may play a role in thereproductive system by causing seminal vesicle hyperplasia. Accordingly,agonists or antagonists to B7-L polypeptide may be useful for thediagnosis or treatment of diseases associated with the reproductivesystem. Examples of such diseases include, but are not limited to,infertility, miscarriage, pre-term labor and delivery, andendometriosis. Other diseases of the reproductive system are encompassedwithin the scope of the invention.

Preferably, the B7-L nucleic acid molecules, polypeptides, and agonistsand antagonists of the present invention are used to treat, diagnose,ameliorate, or prevent diseases associated with T-cell function (e.g.,functioning as a T-cell receptor decoy). For example, antibodies,soluble proteins comprising extracellular domains, or other regulatorsof B7-L polypeptide that result in prolonged or enhanced T-cellactivation can be used to increased the immune response to tumors.

The B7-L nucleic acid molecules, polypeptides, and agonists andantagonists of the present invention may be used in the treatment ofautoimmune disease, graft survival, immune cell activation forinhibiting tumor cell growth, T-cell dependent B-cell mediated diseases,and cancer gene immunotherapy. In one embodiment, agonists of B7-Lpolypeptide function, soluble B7-L polypeptides, or B7-L polypeptidederivatives may be beneficial to alleviate symptoms in diseases withchronic immune cell dysfunction. Autoimmune diseases, such as systemiclupus erythematosis, rheumatoid arthritis, osteoarthritis, immunethrombocytopenic purpura (ITP), and psoriasis, may be treated withagonists of B7-L polypeptide function, soluble B7-L polypeptides, orB7-L polypeptide derivatives. In addition, chronic inflammatorydiseases, such as inflammatory bowel disease (Crohn's disease andulcerative colitis), Grave's disease, Hashimoto's thyroiditis, anddiabetes mellitis, may also be treated with agonists of B7-L polypeptidefunction, soluble B7-L polypeptides, or B7-L polypeptide derivatives.

Agonists of B7-L polypeptide function, soluble B7-L polypeptides, orB7-L polypeptide derivatives may be used as immunosuppressive agents forbone marrow and organ transplantation and may be used to prolong graftsurvival. Such agonists of B7-L polypeptide function, soluble B7-Lpolypeptides, or B 7-L polypeptide derivatives may provide significantadvantages over existing treatments. Bone marrow and organtransplantation therapy must contend with T-cell mediated rejection ofthe foreign cells or tissue by the host. Present therapeutic regimensfor inhibiting T-cell mediated rejection involve treatment with thedrugs cyclosporine or FK506. While drugs are effective, patients sufferfrom serious side effects, including hepatotoxicity, nephrotoxicity, andneurotoxicity. The target for the cyclosporin/FK506 class oftherapeutics is calcineurin, a phosphatase with ubiquitous expression.Agonists of B7-L polypeptide function, soluble B7-L polypeptides, orB7-L polypeptide derivatives may lack the severe side effects observedwith the use of the present immunotherapeutic agents. Agonists of B7-Lpolypeptide function, soluble B7-L polypeptides, or B7-L polypeptidederivatives may be used as immunosuppressive agents for autoimmunedisorders, such as rheumatoid arthritis, osteoarthritis psoriasis,multiple sclerosis, diabetes, and systemic lupus erythematosus. Agonistsof B7-L polypeptide function, soluble B7-L polypeptides, or B7-Lpolypeptide derivatives may also be used to alleviate toxic shocksyndrome, inflammatory bowel disease, allosensitization due to bloodtransfusions, T-cell dependent B-cell mediated diseases, and thetreatment of graft versus host disease.

For instance, many vaccines act by eliciting an effective and specificantibody response. Some vaccines, especially those against intestinalmicroorganisms (e.g., Hepatitis A virus and Salmonella), elicit ashort-lived antibody response. It is desirable to potentiate and prolongthis response in order to increase the effectiveness of the vaccine.Therefore, soluble B7-L polypeptides may serve as vaccine adjuvants.

Conversely, since B7-L may have negative immune regulatory functions,inhibition of B7-L activity using antibodies, small molecules,peptibodies, or other antagonists of B7-L function may result in immuneenhancement and anti-tumor activity.

Anti-viral responses may also be enhanced by activators or agonists ofthe B7-L polypeptide pathway. The enhancement of cellular immunefunctions by B7-L polypeptide antagonists may also be beneficial ineliminating virus-infected cells. In a complementary fashion, B7-Lpolypeptide antagonists may also have effects on humoral immunefunctions that may enhance antibody mediated responses and that mayfunction to help clear free virus from the body.

Conversely, there are a number of clinical conditions that would beameliorated by the inhibition of antibody production. Hypersensitivityis a normally beneficial immune response that is exaggerated orinappropriate, and leads to inflammatory reactions and tissue damage.Hypersensitivity reactions that are antibody-mediated may beparticularly susceptible to antagonism by agonists of B7-L polypeptidefunction, soluble B7-L polypeptides, or B7-L polypeptide derivatives.Allergies, hay fever, asthma, and acute edema cause type Ihypersensitivity reactions, and these reactions may be suppressed byagonists of B7-L polypeptide function, soluble B7-L polypeptides, orB7-L polypeptide derivatives.

Diseases that cause antibody-mediated hypersensitivity reactions,including systemic lupus erythematosis, arthritis (rheumatoid arthritis,reactive arthritis, and psoriatic arthritis), nephropathies(glomerulo-nephritis, membranous, mesangiocapillary, focal segmental,focal necrotizing, crescentic, and proliferative tubulopathies), skindisorders (pemphigus, pemphigoid, and erythema nodosum),endocrinopathies (thyroiditis, Grave's, Hashimoto's, insulin-dependentdiabetes mellitus), various pneumopathies (especially extrinsicalveolitis), various vasculopathies, coeliac disease, with aberrantproduction of IgA, many anemias and thrombocytopenias, Guillain-BarreSyndrome, and myasthenia gravis, may be treated with agonists of B7-Lpolypeptide function, soluble B7-L polypeptides, or B7-L polypeptidederivatives.

In addition, lymphoproliferative disorders, such as multiple myeloma,Waldenstrom's macroglobulinemia, and crioglobulinemias, may be inhibitedby agonists of B7-L polypeptide function, soluble B7-L polypeptides, orB7-L polypeptide derivatives. Finally, graft versus host disease, an“artificial” immune disorder, may benefit from the inhibition ofantibody production by agonists of B7-L polypeptide function, solubleB7-L polypeptides, or B 7-L polypeptide derivatives.

Agonists or antagonists of B7-L polypeptide function may be used(simultaneously or sequentially) in combination with one or morecytokines, growth factors, antibiotics, anti-inflammatories, and/prchemotherapeutic agents as is appropriate for the condition beingtreated.

Other diseases caused by or mediated by undesirable levels of B7-Lpolypeptides are encompassed within the scope of the invention.Undesirable levels include excessive levels of B7-L polypeptides andsub-normal levels of B7-L polypeptides.

B7-L polypeptide is a ligand for a negative regulator of immuneresponses, PD-1 (Nishimura et al., 1999, Immunity 11:141-51). Therefore,agonists of this B7-L polypeptide pathway are likely to inhibit immuneresponses and antagonists of the pathway may enhance immune responses.However, agonists or antagonists of B7-L polypeptide function mayproduce unexpected outcomes due to unknown biological factors.

Uses of B7-L Nucleic Acids and Polypeptides

Nucleic acid molecules of the invention (including those that do notthemselves encode biologically active polypeptides) may be used to mapthe locations of the B7-L gene and related genes on chromosomes. Mappingmay be done by techniques known in the art, such as PCR amplificationand in situ hybridization.

B7-L nucleic acid molecules (including those that do not themselvesencode biologically active polypeptides), may be useful as hybridizationprobes in diagnostic assays to test, either qualitatively orquantitatively, for the presence of a B7-L nucleic acid molecule inmammalian tissue or bodily fluid samples.

Other methods may also be employed where it is desirable to inhibit theactivity of one or more B7-L polypeptides. Such inhibition may beeffected by nucleic acid molecules that are complementary to andhybridize to expression control sequences (triple helix formation) or toB7-L mRNA. For example, antisense DNA or RNA molecules, which have asequence that is complementary to at least a portion of a B7-L gene canbe introduced into the cell. Anti-sense probes may be designed byavailable techniques using the sequence of the B7-L gene disclosedherein. Typically, each such antisense molecule will be complementary tothe start site (5′ end) of each selected B7-L gene. When the antisensemolecule then hybridizes to the corresponding B7-L mRNA, translation ofthis mRNA is prevented or reduced. Anti-sense inhibitors provideinformation relating to the decrease or absence of a B7-L polypeptide ina cell or organism.

Alternatively, gene therapy may be employed to create adominant-negative inhibitor of one or more B7-L polypeptides. In thissituation, the DNA encoding a mutant polypeptide of each selected B7-Lpolypeptide can be prepared and introduced into the cells of a patientusing either viral or non-viral methods as described herein. Each suchmutant is typically designed to compete with endogenous polypeptide inits biological role.

In addition, a B7-L polypeptide, whether biologically active or not, maybe used as an immunogen, that is, the polypeptide contains at least oneepitope to which antibodies may be raised. Selective binding agents thatbind to a B7-L polypeptide (as described herein) may be used for in vivoand in vitro diagnostic purposes, including, but not limited to, use inlabeled form to detect the presence of B7-L polypeptide in a body fluidor cell sample. The antibodies may also be used to prevent, treat, ordiagnose a number of diseases and disorders, including those recitedherein. The antibodies may bind to a B7-L polypeptide so as to diminishor block at least one activity characteristic of a B7-L polypeptide, ormay bind to a polypeptide to increase at least one activitycharacteristic of a B7-L polypeptide (including by increasing thepharmacokinetics of the B7-L polypeptide).

B7-L polypeptides can be used to clone B7-L ligands using an “expressioncloning” strategy. Radiolabeled (¹²⁵Iodine) B7-L polypeptide or“affinity/activity-tagged” B7-L polypeptide (such as an Fc fusion or analkaline phosphatase fusion) can be used in binding assays to identify acell type, cell line, or tissue that expresses a B7-L ligand. RNAisolated from such cells or tissues can then be converted to cDNA,cloned into a mammalian expression vector, and transfected intomammalian cells (e.g. COS or 293) to create an expression library.Radiolabeled or tagged B7-L polypeptide can then be used as an affinityreagent to identify and isolate the subset of cells in this libraryexpressing a B7-L ligand. DNA is then isolated from these cells andtransfected into mammalian cells to create a secondary expressionlibrary in which the fraction of cells expressing the B7-L ligand wouldbe many-fold higher than in the original library. This enrichmentprocess can be repeated iteratively until a single recombinant clonecontaining the B7-L ligand is isolated. Isolation of B7-L ligands isuseful for identifying or developing novel agonists and antagonists ofthe B7-L signaling pathway. Such agonists and antagonists include B7-Lligands, anti-B7-L ligand antibodies, small molecules or antisenseoligonucleotides.

Deposits of cDNA encoding human B7-L polypeptide, subcloned intopGEM-T-Easy (Promega, Madison, Wis.), and having Accession No. PTA 2481,were made with the American Type Culture Collection, 10801 UniversityBoulevard, Manassas, Va. 20110-2209 on Sep. 19, 2000.

The human B7-L nucleic acids of the present invention are also usefultools for isolating the corresponding chromosomal B7-L polypeptidegenes. The human B7-L genomic DNA can be used to identify heritabletissue-degenerating diseases.

The following examples are intended for illustration purposes only, andshould not be construed as limiting the scope of the invention in anyway.

EXAMPLE 1 Cloning of the Human B7-L Polypeptide Genes

Generally, materials and methods as described in Sambrook et al. suprawere used to clone and analyze the genes encoding human and murine B7-Lpolypeptides.

A search of the Genbank-EMBL database was performed using the TBLASTXprogram (http://blast.wustl.edu) and B7-H1 as the query sequence. Ahuman genomic clone (Celera Genomics, Rockville, Md., GA_(—)16817596)was identified as containing nucleic acid sequence encoding a putativenew member of the B7 family. The predicted cDNA sequence for thisputative new member of the B7 family was assembled using a clonecontaining a partial B7-L nucleic acid sequence (GenBank accession no.AK001872).

Plasmid DNA from various cDNA libraries and Marathon cDNA libraries(Clontech, Palo Alto, Calif.) was used as a template in PCRamplifications performed with the primers 2515-27(5′-C-A-T-A-A-T-A-G-A-G-C-A-T-G-G-C-A-G-C-A-A-T-G-T-G-A-C-3′; SEQ ID NO:26) and 2524-63 (5′-G-G-G-T-C-C-T-G-G-A-G-T-G-G-C-T-G-G-T-G-T-T-G-3′;SEQ ID NO: 27). The PCR primers were designed to correspond to sequenceswithin a putative exon in the cDNA sequence identified above. PCRamplifications were performed using standard techniques.

The expected 400 bp PCR fragment was obtained from cDNA librariesgenerated from human fetal stomach, thymus, scalp, calvaria, femur,mesentery, spleen, spinal column, trachea, and placenta. In addition,the expected fragment was obtained in human adult T-cells, pons/medula,and midbrain LVN. Furthermore, the expected fragment was obtained in alymphoma cell line and in colon, breast, ovary, and lung tumors.Marathon cDNA libraries for human fetal adrenal gland, brain, kidney,liver, lung, spleen, and thymus, and adult bone marrow, heart, kidney,liver, lung, pancreas, placenta, retina, skeletal muscle, smallintestine, spleen, testis and thymus also yielded the expected fragment.The 400 bp fragment was also obtained from a sub-pool (E4) of humanmixed-tissue cDNA (the sub-pool containing approximately 15,000 clones).The sub-pool was derived from a custom synthesized library (LTI-FL, LifeTechnologies Inc., Rockville, Md.) optimized for full-length cDNAclones.

The 400 bp fragment obtained in PCR amplifications of human mixed-tissuecDNA was isolated and cloned into the pGEM-T-Easy® vector (Promega,Madison, Wis.). The DNA sequence of a selected clone was determined toconfirm that the sequence of the clone was identical to that of theoriginally identified genomic sequence. The 400 bp fragment was thenexcised from the vector and labeled by incorporation of ³²P-dCTP. Thelabeled fragment was used to screen 150,000 bacterial colonies derivedfrom the 15,000-clone sub-pool of the LTI-FL cDNA library that testedpositive in the prior PCR amplification experiment. Colonies weretransferred from LB/ampicillin plates to nitrocellulose filters,pre-hybridized in 6×SSC, 0.5% SDS, 1×Denhardt's solution and 100 μg/mldenatured salmon sperm DNA for 3 hours at 60° C. Following the additionof 1×10⁶ cpm/ml of the ³²P-labeled probe, hybridization was performedovernight under the same conditions. Filters were washed twice for 30minutes at room temperature in 2×SSC and 0.1% SDS and then twice for 30minutes at 65° C. in 0.1×SSC and 0.1% SDS. Filters were then exposed toX-ray film for 6 hours at −80° C. with intensifying screens.

Several positive colonies were identified in this manner and plasmid DNAfrom these clones was prepared by standard methods. The cDNA insertsfrom these colonies were all approximately 2.2 kb in length. DNAsequence analysis confirmed that the clones contained the putativecoding region of a new member of the B7 family, B7-L, and that thenucleic acid sequence identified in the clones was identical to thatidentified in the genomic clone GA_(—)16817596.

Sequence analysis of the full-length cDNA for human B7-L polypeptideindicated that the gene comprises a 819 bp open reading frame encoding aprotein of 273 amino acids (FIG. 1). Using an HP G100 Protein Sequencer,the amino-terminal end of the mature B7-L polypeptide was sequenced andfound to comprise the amino acid sequence L-F-T-V-T-V-P-K-E-L-Y-I-I-E(SEQ ID NO: 28), thus establishing that B7-L polypeptide possesses asignal peptide of 19 amino acids in length at its amino-terminus (seeFIG. 1; predicted signal peptide indicated by underline).

The nucleic acid sequence identified in the clones, while containing theentire open reading frame, did not contain the full 5′ untranslatedregion of the B7-L transcript. This sequence is determined usingsuccessive rounds of 5′ RACE using the primers 2515-24(5′-G-T-G-G-C-T-C-T-T-T-C-A-C-G-G-T-G-T-G-G-G-G-A-T-G-3′; SEQ ID NO: 29)and 2538-68 (5′-C-C-A-G-T-G-T-C-A-A-A-G-T-T-G-C-A-T-T-C-C-A-G-G-G-T-3′;SEQ ID NO: 30) and the following templates: Marathon cDNA librariesderived from fetal liver, spleen, and thymus, and adult bone marrow,lung, and spleen; cDNA libraries from a lymphoma cell line and ovarytumor; and cDNA libraries from fetal spleen, placenta, and adult T-cellsand spinal column. Standard RACE protocols were employed. Clear bandswere obtained for RACE amplification of the lymphoma cell line, fetalspleen, placenta, and adult T-cells. These products were ligated intothe pGEM-T-Easy® vector. The sequence of the 5′ untranslated region ofthe B7-L transcript is determined by sequencing selected clones fromthese transformation reactions.

The predicted protein product of the B7-L gene is related to the B7family of proteins. These proteins are members of the immunoglobulinsuperfamily and function as regulators of the T-cell mediated immuneresponse. Members of the B7 family of proteins are Type-1 membraneproteins with a small cytoplasmic domain and extracellular regions thatcontain immunoglobulin V (variable) and C (constant) domains. The knownmembers of the B7 family include CD80 (B7-1), CD86 (B7-2), B7-rp1, andB7-H1. B7-1 and B7-2 interact with CD28 and CTLA-4 and are mediators ofthe T cell costimulatory pathway. B7-rp1 binds to a distinct receptor(ICOS; inducible co-stimulator) and is also a stimulator of T-cellproliferation. B7-H1 also co-stimulates T cell proliferation, but doesnot bind CD28, CTLA-4, or ICOS. The protein sequences of this family arepoorly conserved and consequently, are difficult to distinguish fromother related molecules using computational methods, especially whenonly a portion of the full-length coding region sequence is compared.Other proteins exhibiting sequence homology to the B7 family include thebutyrophilins and PRO352. Still more distantly related are the myelinoligodendrocyte proteins (MOGs). FIGS. 2A-2C illustrate an amino acidsequence alignment of the human proteins B7-L polypeptide (GA16817596),CD80 (B7-1), CD86 (B7-2), B7-H1, B7rp-1, PRO352, butyrophilin BTF1,butyrophilin BTF2, butyrophilin BTF4, butyrophilin BTF3, andbutyrophilin.

The full length sequence of the mouse B7-L ortholog was deposited withGenBank on Jun. 1, 1999 (accession no. AF142780). The mouse B7-Lortholog was accurately placed into the B7/butyrophilin family at thetime of deposit. A partial human B7-L cDNA sequence, encoding for 173amino acids from the C-terminal portion of B7-L polypeptide) wasdeposited with GenBank on Feb. 23, 2000 (accession no. AK001872). Thepartial polypeptide encoded by this clone was not assigned to aparticular family of proteins at the time of deposit.

A partial intron-exon structure for the B7-L gene was derived from thegenomic clones GA_(—)43440610, GA_(—)43068628, GA_(—)43068627, andGA_(—)43440600 (Celera Genomics). FIGS. 3A-3E illustrate a portion ofthe genomic nucleotide sequence for human B7-L polypeptide (SEQ ID NO:14). The location of the deduced amino acid sequence of exon 1 (SEQ IDNO: 19) is shown in FIG. 3C. The sequence shown in FIGS. 3A-3E isseparated by a gap of unknown size from the portion of the genomicnucleotide sequence shown in FIG. 4 (SEQ ID NO: 15). The sequence shownin FIG. 4 is separated by a masked sequence of approximately 2400 basesfrom the genomic nucleotide sequence shown in FIGS. 5A-5F (SEQ ID NO:16). The location of the deduced amino acid sequence of exon 2 (SEQ IDNO: 20) is shown in FIG. 5D. The sequence shown in FIGS. 5A-5F isseparated by a gap of approximately 9600 bases from the genomicnucleotide sequence shown in FIGS. 6A-6B (SEQ ID NO: 17). The locationof the deduced amino acid sequence of exon 3 (SEQ ID NO: 21) is shown in6A. The sequence shown in FIGS. 6A-6B is separated by a masked sequenceof approximately 720 bases from the genomic nucleotide sequence shown inFIGS. 7A-7M (SEQ ID NO: 18). The locations of the deduced amino acidsequence of exons 4 (SEQ ID NO: 22), 5 (SEQ ID NO: 23), and 6 are shownin 7D-7E, 7H, and 7L, respectively.

EXAMPLE 2 B7-L mRNA Expression

A multiple human tissue Northern blot (Clontech) was hybridized to an874 bp probe corresponding to nucleotides 33-906 of the human B7-L cDNAsequence. The probe was radioactively labeled using a Prime-It RmTRandom Primer Labeling kit (Stratagene) according to the manufacturer'sinstructions. Northern blots were hybridized and washed according to themanufacturer's instructions, and then exposed to autoradiography. FIG. 8illustrates the results of the Northern blot analysis.

The expression of B7-L mRNA is localized by in situ hybridization. Apanel of normal embryonic and adult mouse tissues is fixed in 4%paraformaldehyde, embedded in paraffin, and sectioned at 5 μm. Sectionedtissues are permeabilized in 0.2 M HCl, digested with Proteinase K, andacetylated with triethanolamine and acetic anhydride. Sections areprehybridized for 1 hour at 60° C. in hybridization solution (300 mMNaCl, 20 mM Tris-HCl, pH 8.0, 5 mM EDTA, 1×Denhardt's solution, 0.2%SDS, 10 mM DTT, 0.25 mg/ml tRNA, 25 μg/ml polyA, 25 μg/ml polyC and 50%formamide) and then hybridized overnight at 60° C. in the same solutioncontaining 10% dextran and 2×10⁴ cpm/μl of a ³³P-labeled antisenseriboprobe complementary to the human B7-L gene. The riboprobe isobtained by in vitro transcription of a clone containing human B7-L cDNAsequences using standard techniques.

Following hybridization, sections are rinsed in hybridization solution,treated with RNaseA to digest unhybridized probe, and then washed in0.1×SSC at 55° C. for 30 minutes. Sections are then immersed in NTB-2emulsion (Kodak, Rochester, N.Y.), exposed for 3 weeks at 4° C.,developed, and counterstained with hematoxylin and eosin. Tissuemorphology and hybridization signal are simultaneously analyzed bydarkfield and standard illumination for brain (one sagittal and twocoronal sections), gastrointestinal tract (esophagus, stomach, duodenum,jejunum, ileum, proximal colon, and distal colon), pituitary, liver,lung, heart, spleen, thymus, lymph nodes, kidney, adrenal, bladder,pancreas, salivary gland, male and female reproductive organs (ovary,oviduct, and uterus in the female; and testis, epididymus, prostate,seminal vesicle, and vas deferens in the male), BAT and WAT(subcutaneous, peri-renal), bone (femur), skin, breast, and skeletalmuscle.

EXAMPLE 3 Production of B7-L Polypeptides A. Expression of B7-LPolypeptides in Bacteria

PCR is used to amplify template DNA sequences encoding a B7-Lpolypeptide using primers corresponding to the 5′ and 3′ ends of thesequence. The amplified DNA products may be modified to containrestriction enzyme sites to allow for insertion into expression vectors.PCR products are gel purified and inserted into expression vectors usingstandard recombinant DNA methodology. An exemplary vector, such aspAMG21 (ATCC no. 98113) containing the lux promoter and a gene encodingkanamycin resistance is digested with Bam HI and Nde I for directionalcloning of inserted DNA. The ligated mixture is transformed into an E.coli host strain by electroporation and transformants are selected forkanamycin resistance. Plasmid DNA from selected colonies is isolated andsubjected to DNA sequencing to confirm the presence of the insert.

Transformed host cells are incubated in 2×YT medium containing 30 μlkanamycin at 30° C. prior to induction. Gene expression is induced bythe addition of N-(3-oxohexanoyl)-dl-homoserine lactone to a finalconcentration of 30 ng/mL followed by incubation at either 30° C. or 37°C. for six hours. The expression of B7-L polypeptide is evaluated bycentrifugation of the culture, resuspension and lysis of the bacterialpellets, and analysis of host cell proteins by SDS-polyacrylamide gelelectrophoresis.

Inclusion bodies containing B7-L polypeptide are purified as follows.Bacterial cells are pelleted by centrifugation and resuspended in water.The cell suspension is lysed by sonication and pelleted bycentrifugation at 195,000×g for 5 to 10 minutes. The supernatant isdiscarded, and the pellet is washed and transferred to a homogenizer.The pellet is homogenized in 5 mL of a Percoll solution (75% liquidPercoll and 0.15 M NaCl) until uniformly suspended and then diluted andcentrifuged at 21,600×g for 30 minutes. Gradient fractions containingthe inclusion bodies are recovered and pooled. The isolated inclusionbodies are analyzed by SDS-PAGE.

A single band on an SDS polyacrylamide gel corresponding to E.coli-produced B7-L polypeptide is excised from the gel, and theN-terminal amino acid sequence is determined essentially as described byMatsudaira et al., 1987, J. Biol. Chem. 262:10-35.

B. Expression of B7-L Polypeptide in Mammalian Cells

PCR is used to amplify template DNA sequences encoding a B7-Lpolypeptide using primers corresponding to the 5′ and 3′ ends of thesequence. The amplified DNA products may be modified to containrestriction enzyme sites to allow for insertion into expression vectors.PCR products are gel purified and inserted into expression vectors usingstandard recombinant DNA methodology. An exemplary expression vector,pCEP4 (Invitrogen, Carlsbad, Calif.), that contains an Epstein-Barrvirus origin of replication, may be used for the expression of B7-Lpolypeptides in 293-EBNA-1 cells. Amplified and gel purified PCRproducts are ligated into pCEP4 vector and introduced into 293-EBNAcells by lipofection. The transfected cells are selected in 100 μg/mLhygromycin and the resulting drug-resistant cultures are grown toconfluence. The cells are then cultured in serum-free media for 72hours. The conditioned media is removed and B7-L polypeptide expressionis analyzed by SDS-PAGE.

B7-L polypeptide expression may be detected by silver staining.Alternatively, B7-L polypeptide is produced as a fusion protein with anepitope tag, such as an IgG constant domain or a FLAG epitope, which maybe detected by Western blot analysis using antibodies to the peptidetag.

B7-L polypeptides may be excised from an SDS-polyacrylamide gel, or B7-Lfusion proteins are purified by affinity chromatography to the epitopetag, and subjected to N-terminal amino acid sequence analysis asdescribed herein.

C. Expression of B7-L Polypeptide/Fc Fusion Protein in Mammalian Cells

A 660 bp fragment of B7-L cDNA, encoding 220 amino acids at theamino-terminal end of B7-L polypeptide, and which includes the signalpeptide and extracellular domain of B7-L polypeptide, was amplified byPCR using suitable primers and standard techniques. Plasmid DNA isolatedfrom the custom synthesized library described in Example 1 was used as atemplate in the PCR amplifications.

The 660 bp fragment was then cloned into the expression vector,pCEP4/Fc, which contains nucleic acid sequence encoding thecarboxyl-terminal 235 amino acids of human Fc (IgG-1). Colonies wereselected following transformation of bacterial cells, and pCEP4-B7-L/Fcplasmid DNA was isolated using standard techniques.

Isolated plasmid DNA was used to transfect 293-EBNA-1 cells using FuGENE6 Transfection Reagent (Roche Molecular Biochemicals, Indianapolis,Ind.) according to the manufacturer's instructions. Followingtransfection, the cells were cultured at 37° C. in DMEM medium,supplemented with 10% fetal bovine serum, for 24 hours, and thentransferred to DMEM serum-free medium and grown at 37° C. for 5 days.The B7-L polypeptide/Fc fusion protein was purified from the conditionedmedia on a HiTrap Protein A Column (Amersham Pharmacia Biotech,Piscataway, N.J.) according to the manufacturer's instructions, and thefusion protein was then dialyzed in PBS. The concentration of thepurified protein was measured using Coomassie® Plus Protein AssayReagent (Pierce, Rockford, Ill.) and BSA as a standard, according to themanufacturer's instructions.

EXAMPLE 4 Identification of B7-L Polypeptide as a Novel PD-1 Ligand

To determine whether B7-L polypeptide functions in one of the knownB7-mediated co-stimulatory pathways, FACS analysis was performed on CHOD-cells expressing CD28, CRP-1/ICOS, or PD-1 following treatment with aB7-L polypeptide/Fc fusion protein.

The full-length nucleic acid sequence encoding murine PD-1 (mPD-1;Ishida et al., 1992, EMBO J. 11:3887-95), and including the native PD-1signal peptide, was obtained by PCR amplification of a murine activatedspleen lymphocyte cDNA library using primers incorporating Hind III andSal I restriction endonuclease sites. The resulting PCR product wasdigested with Hind III and Sal I and then ligated into the pDSRa-19vector. Following transformation into bacterial cells, clones wereselected and sequenced. A clone containing the full-length mPD-1 cDNAsequence (clone 1.5) was linearized using the restriction endonucleasePvu I, and the linearized plasmid was used to transfect CHO D-cells bythe calcium phosphate method. Transfected CHO D-cells were cultured, andindividual colonies isolated via ring cloning several weeks later. Ahigh expressing transfectant (clone 3.36) was identified for its abilityto specifically bind the B7-H1/Fc fusion protein (Dong et al., 1999,Nat. Med. 5:1365-69).

CHO D-cells expressing vector alone, mPD-1 (clone 3.36), human CD28, ormCRP1/ICOS (clone 1.41; Yoshinaga et al., 1999, Nature 402:827-32) werecultured in T175 flasks in DMEM supplemented with 5% dFBS, 1×PSG, and1×NEAA. Cells were released from the culture flasks using CellDissociation Solution (Sigma, St. Louis, Mo.), diluted in wash buffer(PBS containing 0.5% BSA), and then counted.

Approximately 3.0×10⁵ cells in 0.1 ml of media were reacted for 1 houron ice with 1 μg of purified murine CRP1/Fc, human B7-L polypeptide/Fc,murine B7rp-1/Fc, or murine B7-2/Fc. CHO D-cells were also incubatedwith murine B7-H1/Fc as described above, except that the cells wereexposed to 10 μg of fusion protein in 1 ml of serum-free conditionedmedia harvested from CHO D-cells expressing mB7-H1/Fc. Followingincubation, cells were diluted with 5 ml of wash buffer, centrifuged,and then washed twice in 5 ml of wash buffer. The cells were thenresuspended in 100 μl of wash buffer containing 10 μg/ml of a goatanti-human IgG Fc-specific FITC-conjugated detection antibody (Chemicon,Temecula Calif.). The cells were allowed to react for 30 minutes on ice,and then were washed as described above. Following washing, cells wereresuspended in a final volume of 1 ml wash buffer and then were analyzedusing a FACS Star (Beckman Dickinson, Franklin Lakes, N.J.).

As shown in FIG. 9, B7-L polypeptide specifically binds to the PD-1receptor, but not the CD28 or CRP-1/ICOS receptors. The fusion proteinsB7-2/Fc and B7rp-1/Fc bound to the CD28 and CRP-1/ICOS receptors, asexpected. As B7-H1 was also shown to specifically bind the PD-1 receptor(FIG. 9B), FACS analysis indicates that both B7-L polypeptide and B7-H1are ligands for the PD-1 receptor. Since PD-1 is a negative regulator ofT-cell proliferation (Nishimura et al., 1999, Immunity 11:141-51),activation of this pathway via soluble B7-L polypeptide may result in areduced immune response. Conversely, antagonistic antibodies to B7-Lpolypeptide may increase immune functions.

EXAMPLE 5 Inhibition of T-Cell Proliferation by B7-L Polypeptide

To determine whether B7-L polypeptide plays a role in T-cellproliferation, human T-cell proliferation assays were performed usingB7-L polypeptide/Fc fusion proteins. Highly purified human T-cells (>98%CD3+) were isolated by negative selection of fresh or thawed,adherence-depleted, peripheral blood mononuclear cells (PBMCs) using thePan T-cell Isolation kit (Miltenyi Biotec, Auburn, Calif.). Roundbottom, 96-well, cell culture plates were precoated overnight at 4° C.with 0.5 or 1.5 μg/ml of anti-CD3 antibody (PharMingen, San Diego,Calif.), 10 μg/ml anti-human IgG Fc (Sigma), and PBS, in a volume of 0.1ml. The precoating solution was removed, the plates were washed oncewith PBS, and 0.1 ml of the B7-L polypeptide/Fc, B7-2/Fc or B7rp-1/Fcfusion proteins diluted to 20 μg/ml in RPMI 1640 supplemented with 10%FCS media, or media alone, was added to the wells. The plates were thenincubated for 4 hours at 37° C. Following incubation, the media wasremoved and 0.2 ml of the purified T-cells (containing 10×10⁵ cells) wasadded to each precoated well. The plates were then incubated for 48hours at 37° C. Following incubation, 1 μCi/well of [³H]thymidine wasadded to each well and the cultures were incubated for an additional 18hrs at 37° C. The cells were then harvested and the counts per minute(CPM) measured.

As shown in FIG. 10, the B7-L polypeptide/Fc fusion protein was capableof inhibiting anti-CD3 mediated T-cell proliferation at eitherconcentration of anti-CD3 antibody. Conversely, the B7rp-1/Fc andB7-1/Fc fusion proteins were shown to co-stimulate T-cell proliferationunder the same conditions. These results indicate that B7-L polypeptideis a negative regulator of T-cell proliferation. Furthermore, theseresults suggest that the B7-L polypeptide/Fc fusion protein, or othersoluble B7-L polypeptide derivatives, may be used to inhibit immunefunction, thereby providing favorable therapeutic outcomes. In vitroassays, such as the assay described herein could also be used to screenfor antibodies, soluble proteins, or small molecule inhibitors of B7-Lpolypeptide activity.

EXAMPLE 6 B7-L Polypeptide Receptors are Expressed on Human PeripheralBlood Mononuclear Cells

FACS analysis was used to identify B7-L polypeptide receptors on T- andB-cells in human PBMC. Using Ficoll-Paque (Amersham Pharmacia Biotech)gradient centrifugation, PBMC were purified from blood obtained fromhealthy human volunteers, and the cells stimulated by incubation in 10μg/ml lipopolysaccharide (LPS) for 3 days. Following LPS treatment,5×10⁵ cells in a volume of 0.2 ml were blocked with 100 μg/ml human IgGFc for 10 minutes on ice. The cells were then incubated with 10 μg/ml ofvarious biotinylated Fc fusion proteins (or suitable controls) for 30minutes on ice. Following incubation with Fc fusion proteins, the cellsamples indicated in FIG. 11 were incubated with anti-CD3 (PharMingen)or anti-CD19 (Becton Dickinson) antibodies for 30 minutes on ice.Following incubation, cells were washed twice in wash buffer (PBScontaining 0.5% BSA), and then were stained with FITC avidin (1:100dilution) for 30 minutes on ice. The cells were resuspended in 1 ml washbuffer and were analyzed on a FACS Star.

As shown in FIG. 11, the B7-L polypeptide/Fc protein bound tosignificant populations of peripheral blood mononuclear cells (PBMC).Double-staining with B7-L polypeptide/Fc fusion protein and T-cell (CD3)or B-cell (CD19) markers indicated that a portion of the cells to whichB7-L polypeptide/Fc fusion protein bound were T-cells and B-cells.Significant numbers of the B7-L polypeptide receptor-expressing cells,however, were also shown not to be T-cells or B-cells. Therefore,non-lymphocytes, as well as, lymphocytes in PMBC may be regulated byB7-L polypeptide. This pattern of binding is consistent with that withthe pattern of PD-1 expression (Ishida et al., 1992, EMBO J.11:3887-95).

EXAMPLE 7 Production of Anti-B7-L Polypeptide Antibodies

Antibodies to B7-L polypeptides may be obtained by immunization withpurified protein or with B7-L peptides produced by biological orchemical synthesis. Suitable procedures for generating antibodiesinclude those described in Hudson and Bay, Practical Immunology (2nded., Blackwell Scientific Publications).

In one procedure for the production of antibodies, animals (typicallymice or rabbits) are injected with a B7-L antigen (such as a B7-Lpolypeptide), and those with sufficient serum titer levels as determinesby ELISA are selected for hybridoma production. Spleens of immunizedanimals are collected and prepared as single cell suspensions from whichsplenocytes are recovered. The splenocytes are fused to mouse myelomacells (such as Sp2/0-Ag14 cells), are first incubated in DMEM with 200U/mL penicillin, 200 μg/ml streptomycin sulfate, and 4 mM glutamine, andare then incubated in HAT selection medium (hypoxanthine, aminopterin,and thymidine). After selection, the tissue culture supernatants aretaken from each fusion well and tested for anti-B7-L antibody productionby ELISA.

Alternative procedures for obtaining anti-B7-L antibodies may also beemployed, such as the immunization of transgenic mice harboring human Igloci for production of human antibodies, and the screening of syntheticantibody libraries, such as those generated by mutagenesis of anantibody variable domain.

EXAMPLE 8 Expression of B7-L Polypeptide in Transgenic Mice

To assess the biological activity of B7-L polypeptide, a constructencoding a B7-L polypeptide/Fc fusion protein under the control of aliver specific APQE promoter is prepared. The delivery of this constructis expected to cause pathological changes that are informative as to thefunction of B7-L polypeptide. Similarly, a construct containing thefull-length B7-L polypeptide under the control of the beta actinpromoter is prepared. The delivery of this construct is expected toresult in ubiquitous expression.

To generate these constructs, PCR is used to amplify template DNAsequences encoding a B7-L polypeptide using primers that correspond tothe 5′ and 3′ ends of the desired sequence and which incorporaterestriction enzyme sites to permit insertion of the amplified productinto an expression vector. Following amplification, PCR products are gelpurified, digested with the appropriate restriction enzymes, and ligatedinto an expression vector using standard recombinant DNA techniques. Forexample, amplified B7-L polypeptide sequences can be cloned into anexpression vector under the control of the human β-actin promoter asdescribed by Graham et al., 1997, Nature Genetics, 17:272-74 and Ray etal., 1991, Genes Dev. 5:2265-73.

Following ligation, reaction mixtures are used to transform an E. colihost strain by electroporation and transformants are selected for drugresistance. Plasmid DNA from selected colonies is isolated and subjectedto DNA sequencing to confirm the presence of an appropriate insert andabsence of mutation. The B7-L polypeptide expression vector is purifiedthrough two rounds of CsCl density gradient centrifugation, cleaved witha suitable restriction enzyme, and the linearized fragment containingthe B7-L polypeptide transgene is purified by gel electrophoresis. Thepurified fragment is resuspended in 5 mM Tris, pH 7.4, and 0.2 mM EDTAat a concentration of 2 mg/mL.

Single-cell embryos from BDF1×BDF1 bred mice are injected as described(International Pub. No. WO 97/23614). Embryos are cultured overnight ina CO₂ incubator and 15-20 two-cell embryos are transferred to theoviducts of a pseudopregnant CD1 female mice. Offspring obtained fromthe implantation of microinjected embryos are screened by PCRamplification of the integrated transgene in genomic DNA samples asfollows. Ear pieces are digested in 20 mL ear buffer (20 mM Tris, pH8.0, 10 mM EDTA, 0.5% SDS, and 500 mg/mL proteinase K) at 55° C.overnight. The sample is then diluted with 200 mL of TE, and 2 mL of theear sample is used in a PCR reaction using appropriate primers.

At 8 weeks of age, transgenic founder animals and control animals aresacrificed for necropsy and pathological analysis. Portions of spleenare removed and total cellular RNA isolated from the spleens using theTotal RNA Extraction Kit (Qiagen) and transgene expression determined byRT-PCR. RNA recovered from spleens is converted to cDNA using theSuperScript™ Preamplification System (Gibco-BRL) as follows. A suitableprimer, located in the expression vector sequence and 3′ to the B7-Lpolypeptide transgene, is used to prime cDNA synthesis from thetransgene transcripts. Ten mg of total spleen RNA from transgenicfounders and controls is incubated with 1 mM of primer for 10 minutes at70° C. and placed on ice. The reaction is then supplemented with 10 mMTris-HCl, pH 8.3, 50 mM KCl, 2.5 mM MgCl₂, 10 mM of each dNTP, 0.1 mMDTT, and 200 U of SuperScript II reverse transcriptase. Followingincubation for 50 minutes at 42° C., the reaction is stopped by heatingfor 15 minutes at 72° C. and digested with 2 U of RNase H for 20 minutesat 37° C. Samples are then amplified by PCR using primers specific for B7-L polypeptide.

EXAMPLE 9 Biological Activity of B7-L Polypeptide in Transgenic Mice

Prior to euthanasia, transgenic animals are weighed, anesthetized byisofluorane and blood drawn by cardiac puncture. The samples aresubjected to hematology and serum chemistry analysis. Radiography isperformed after terminal exsanguination. Upon gross dissection, majorvisceral organs are subject to weight analysis.

Following gross dissection, tissues (i.e., liver, spleen, pancreas,stomach, the entire gastrointestinal tract, kidney, reproductive organs,skin and mammary glands, bone, brain, heart, lung, thymus, trachea,esophagus, thyroid, adrenals, urinary bladder, lymph nodes and skeletalmuscle) are removed and fixed in 10% buffered Zn-Formalin forhistological examination. After fixation, the tissues are processed intoparaffin blocks, and 3 mm sections are obtained. All sections arestained with hematoxylin and exosin, and are then subjected tohistological analysis.

The spleen, lymph node, and Peyer's patches of both the transgenic andthe control mice are subjected to immunohistology analysis with B celland T cell specific antibodies as follows. The formalin fixed paraffinembedded sections are deparaffinized and hydrated in deionized water.The sections are quenched with 3% hydrogen peroxide, blocked withProtein Block (Lipshaw, Pittsburgh, Pa.), and incubated in ratmonoclonal anti-mouse B220 and CD3 (Harlan, Indianapolis, Ind.).Antibody binding is detected by biotinylated rabbit anti-ratimmunoglobulins and peroxidase conjugated streptavidin (BioGenex, SanRamon, Calif.) with DAB as a chromagen (BioTek, Santa Barbara, Calif.).Sections are counterstained with hematoxylin.

After necropsy, MLN and sections of spleen and thymus from transgenicanimals and control littermates are removed. Single cell suspensions areprepared by gently grinding the tissues with the flat end of a syringeagainst the bottom of a 100 mm nylon cell strainer (Becton Dickinson,Franklin Lakes, N.J.). Cells are washed twice, counted, andapproximately 1×10⁶ cells from each tissue are then incubated for 10minutes with 0.5 μg CD 16/32(FcγIII/II) Fc block in a 20 μL volume.Samples are then stained for 30 minutes at 2-8° C. in a 100 μL volume ofPBS (lacking Ca⁺ and Mg⁺), 0.1% bovine serum albumin, and 0.01% sodiumazide with 0.5 μg antibody of FITC or PE-conjugated monoclonalantibodies against CD90.2 (Thy-1.2), CD45R (B220), CD11b (Mac-1), Gr-1,CD4, or CD8 (PharMingen, San Diego, Calif.). Following antibody binding,the cells are washed and then analyzed by flow cytometry on a FACScan(Becton Dickinson).

While the present invention has been described in terms of the preferredembodiments, it is understood that variations and modifications willoccur to those skilled in the art. Therefore, it is intended that theappended claims cover all such equivalent variations that come withinthe scope of the invention as claimed.

1. An isolated nucleic acid molecule comprising a nucleotide sequenceselected from the group consisting of: (a) the nucleotide sequence asset forth in SEQ ID NO: 1; (b) the nucleotide sequence of the DNA insertin ATCC Deposit No. PTA 2481; (c) a nucleotide sequence encoding thepolypeptide as set forth in SEQ ID NO: 2; (d) a nucleotide sequence thathybridizes under at least moderately stringent conditions to thecomplement of the nucleotide sequence of any of (a)-(c); and (e) anucleotide sequence complementary to the nucleotide sequence of any of(a)-(c).
 2. An isolated nucleic acid molecule comprising a nucleotidesequence selected from the group consisting of: (a) a nucleotidesequence encoding a polypeptide that is at least about 70 percentidentical to the polypeptide as set forth in SEQ ID NO: 2 or thenucleotide sequence of the DNA insert in ATCC Deposit No. PTA 2481,wherein the encoded polypeptide has an activity of the polypeptide setforth in SEQ ID NO: 2; (b) a nucleotide sequence encoding an allelicvariant or splice variant of the nucleotide sequence as set forth in SEQID NO: 1, the nucleotide sequence of the DNA insert in ATCC Deposit No.PTA 2481, or the nucleotide sequence of (a); (c) a region of thenucleotide sequence of SEQ ID NO: 1, the nucleotide sequence of the DNAinsert in ATCC Deposit No. PTA 2481, or the nucleotide sequence of (a)or (b) encoding a polypeptide fragment of at least about 25 amino acidresidues, wherein the polypeptide fragment has an activity of theencoded polypeptide as set forth in SEQ ID NO: 2, or is antigenic; (d) aregion of the nucleotide sequence of SEQ ID NO: 1, the nucleotidesequence of the DNA insert in ATCC Deposit No. PTA 2481, or thenucleotide sequence of any of (a)-(c) comprising a fragment of at leastabout 16 nucleotides; (e) a nucleotide sequence that hybridizes under atleast moderately stringent conditions to the complement of thenucleotide sequence of any of (a)-(d); and (f) a nucleotide sequencecomplementary to the nucleotide sequence of any of (a)-(d).
 3. Anisolated nucleic acid molecule comprising a nucleotide sequence selectedfrom the group consisting of: (a) a nucleotide sequence encoding apolypeptide as set forth in SEQ ID NO: 2 with at least one conservativeamino acid substitution, wherein the encoded polypeptide has an activityof the polypeptide set forth in SEQ ID NO: 2; (b) a nucleotide sequenceencoding a polypeptide as set forth in SEQ ID NO: 2 with at least oneamino acid insertion, wherein the encoded polypeptide has an activity ofthe polypeptide set forth in SEQ ID NO: 2; (c) a nucleotide sequenceencoding a polypeptide as set forth in SEQ ID NO: 2 with at least oneamino acid deletion, wherein the encoded polypeptide has an activity ofthe polypeptide set forth in SEQ ID NO: 2; (d) a nucleotide sequenceencoding a polypeptide as set forth in SEQ ID NO: 2 that has a C- and/orN-terminal truncation, wherein the encoded polypeptide has an activityof the polypeptide set forth in SEQ ID NO: 2; (e) a nucleotide sequenceencoding a polypeptide as set forth in SEQ ID NO: 2 with at least onemodification selected from the group consisting of amino acidsubstitutions, amino acid insertions, amino acid deletions, C-terminaltruncation, and N-terminal truncation, wherein the encoded polypeptidehas an activity of the polypeptide set forth in SEQ ID NO: 2; (f) anucleotide sequence of any of (a)-(e) comprising a fragment of at leastabout 16 nucleotides; (g) a nucleotide sequence that hybridizes under atleast moderately stringent conditions to the complement of thenucleotide sequence of any of (a)-(f); and (h) a nucleotide sequencecomplementary to the nucleotide sequence of any of (a)-(e).
 4. A vectorcomprising the nucleic acid molecule of any of claims 1, 2, or
 3. 5. Ahost cell comprising the vector of claim
 4. 6. The host cell of claim 5that is a eukaryotic cell.
 7. The host cell of claim 5 that is aprokaryotic cell.
 8. A process of producing a B7-L polypeptidecomprising culturing the host cell of claim 5 under suitable conditionsto express the polypeptide, and optionally isolating the polypeptidefrom the culture.
 9. A polypeptide produced by the process of claim 8.10. The process of claim 8, wherein the nucleic acid molecule comprisespromoter DNA other than the promoter DNA for the native B7-L polypeptideoperatively linked to the DNA encoding the B7-L polypeptide.
 11. Theisolated nucleic acid molecule according to claim 2, wherein the percentidentity is determined using a computer program selected from the groupconsisting of GAP, BLASTN, FASTA, BLASTA, BLASTX, BestFit, and theSmith-Waterman algorithm.
 12. A process for determining whether acompound inhibits B7-L polypeptide activity or B7-L polypeptideproduction comprising exposing a cell according to any of claims 5, 6,or 7 to the compound and measuring B7-L polypeptide activity or B7-Lpolypeptide production in said cell.
 13. An isolated polypeptidecomprising the amino acid sequence selected from the group consistingof: (a) the amino acid sequence as set forth in SEQ ID NO: 2; and (b)the amino acid sequence encoded by the DNA insert of ATCC Deposit No.PTA
 2481. 14. An isolated polypeptide comprising an amino acid sequenceselected from the group consisting of (a) the amino acid sequence as setforth in SEQ ID NO: 3, optionally further comprising an amino-terminalmethionine; (b) an amino acid sequence for an ortholog of SEQ ID NO: 2;(c) an amino acid sequence that is at least about 70 percent identicalto the amino acid sequence of SEQ ID NO: 2 or the amino acid sequenceencoded by the DNA insert of ATCC Deposit No. PTA 2481, wherein thepolypeptide has an activity of the polypeptide set forth in SEQ ID NO:2; (d) a fragment of the amino acid sequence set forth in SEQ ID NO: 2or the amino acid sequence encoded by the DNA insert of ATCC Deposit No.PTA 2481 comprising at least about 25 amino acid residues, wherein thefragment has an activity of the polypeptide set forth in SEQ ID NO: 2,or is antigenic; and (e) an amino acid sequence for an allelic variantor splice variant of the amino acid sequence as set forth in SEQ ID NO:2, the amino acid sequence encoded by the DNA insert of ATCC Deposit No.PTA 2481, or the amino acid sequence of any of (a)-(c).
 15. An isolatedpolypeptide comprising an amino acid sequence selected from the groupconsisting of: (a) the amino acid sequence as set forth in SEQ ID NO: 2with at least one conservative amino acid substitution, wherein thepolypeptide has an activity of the polypeptide set forth in SEQ ID NO:2; (b) the amino acid sequence as set forth in SEQ ID NO: 2 with atleast one amino acid insertion, wherein the polypeptide has an activityof the polypeptide set forth in SEQ ID NO: 2; (c) the amino acidsequence as set forth in SEQ ID NO: 2 with at least one amino aciddeletion, wherein the polypeptide has an activity of the polypeptide setforth in SEQ ID NO: 2; (d) the amino acid sequence as set forth in SEQID NO: 2 that has a C- and/or N-terminal truncation, wherein thepolypeptide has an activity of the polypeptide set forth in SEQ ID NO:2; and (e) the amino acid sequence as set forth in SEQ ID NO: 2 with atleast one modification selected from the group consisting of amino acidsubstitutions, amino acid insertions, amino acid deletions, C-terminaltruncation, and N-terminal truncation, wherein the polypeptide has anactivity of the polypeptide set forth in SEQ ID NO:
 2. 16. An isolatedpolypeptide encoded by the nucleic acid molecule of any of claims 1, 2,or 3, wherein the polypeptide has an activity of the polypeptide setforth in SEQ ID NO:
 2. 17. The isolated polypeptide according to claim14, wherein the percent identity is determined using a computer programselected from the group consisting of GAP, BLASTP, FASTA, BLASTA,BLASTX, BestFit, and the Smith-Waterman algorithm.
 18. A selectivebinding agent or fragment thereof that specifically binds thepolypeptide of any of claims 13, 14, 15, or
 56. 19. The selectivebinding agent or fragment thereof of claim 18 that specifically bindsthe polypeptide comprising the amino acid sequence as set forth in SEQID NO: 2, or a fragment thereof.
 20. The selective binding agent ofclaim 18 that is an antibody or fragment thereof.
 21. The selectivebinding agent of claim 18 that is a humanized antibody.
 22. Theselective binding agent of claim 18 that is a human antibody or fragmentthereof.
 23. The selective binding agent of claim 18 that is apolyclonal antibody or fragment thereof.
 24. The selective binding agentclaim 18 that is a monoclonal antibody or fragment thereof.
 25. Theselective binding agent of claim 18 that is a chimeric antibody orfragment thereof.
 26. The selective binding agent of claim 18 that is aCDR-grafted antibody or fragment thereof.
 27. The selective bindingagent of claim 18 that is an antiidiotypic antibody or fragment thereof.28. The selective binding agent of claim 18 that is a variable regionfragment.
 29. The variable region fragment of claim 28 that is a Fab ora Fab′ fragment.
 30. A selective binding agent or fragment thereofcomprising at least one complementarity determining region withspecificity for a polypeptide having the amino acid sequence of SEQ IDNO:
 2. 31. The selective binding agent of claim 18 that is bound to adetectable label.
 32. The selective binding agent of claim 18 thatantagonizes B7-L polypeptide biological activity.
 33. A method fortreating, preventing, or ameliorating a B7-L polypeptide-relateddisease, condition, or disorder comprising administering to a patient aneffective amount of a selective binding agent according to claim
 18. 34.A selective binding agent produced by immunizing an animal with apolypeptide comprising an amino acid sequence of SEQ ID NO:
 2. 35. Ahybridoma that produces a selective binding agent capable of binding apolypeptide according to any of claims 13, 14, 15, or
 56. 36. A methodof detecting or quantitating the amount of B7-L polypeptide using theanti-B7-L antibody or fragment of claim
 18. 37. A composition comprisingthe polypeptide of any of claims 13, 14, 15, or 56, and apharmaceutically acceptable formulation agent.
 38. The composition ofclaim 37, wherein the pharmaceutically acceptable formulation agent is acarrier, adjuvant, solubilizer, stabilizer, or anti-oxidant.
 39. Thecomposition of claim 37 wherein the polypeptide comprises the amino acidsequence as set forth in SEQ ID NO:
 3. 40. A polypeptide comprising aderivative of the polypeptide of any of claims 13, 14, 15, or
 56. 41.The polypeptide of claim 40 that is covalently modified with awater-soluble polymer.
 42. The polypeptide of claim 41, wherein thewater-soluble polymer is selected from the group consisting ofpolyethylene glycol, monomethoxy-polyethylene glycol, dextran,cellulose, poly-(N-vinyl pyrrolidone) polyethylene glycol, propyleneglycol homopolymers, polypropylene oxide/ethylene oxide co-polymers,polyoxyethylated polyols, and polyvinyl alcohol.
 43. A compositioncomprising a nucleic acid molecule of any of claims 1, 2, or 3 and apharmaceutically acceptable formulation agent.
 44. The composition ofclaim 43, wherein said nucleic acid molecule is contained in a viralvector.
 45. A viral vector comprising a nucleic acid molecule of any ofclaims 1, 2, or
 3. 46. A fusion polypeptide comprising the polypeptideof any of claims 13, 14, 15, or 56 fused to a heterologous amino acidsequence.
 47. The fusion polypeptide of claim 46, wherein theheterologous amino acid sequence is an IgG constant domain or fragmentthereof.
 48. A method for treating, preventing, or ameliorating amedical condition comprising administering to a patient the polypeptideof any of claims 13, 14, 15, or 56, or the polypeptide encoded by thenucleic acid of any of claims 1, 2, or
 3. 49. A method of diagnosing apathological condition or a susceptibility to a pathological conditionin a subject comprising: (a) determining the presence or amount ofexpression of the polypeptide of any of claims 13, 14, 15, or 56, or thepolypeptide encoded by the nucleic acid molecule of any of claims 1, 2,or 3 in a sample; and (b) diagnosing a pathological condition or asusceptibility to a pathological condition based on the presence oramount of expression of the polypeptide.
 50. A device, comprising: (a) amembrane suitable for implantation; and (b) cells encapsulated withinsaid membrane, wherein said cells secrete a protein of any of claims 13,14, 15, or 56; and said membrane is permeable to said protein andimpermeable to materials detrimental to said cells.
 51. A method ofidentifying a compound that binds to a B7-L polypeptide comprising: (a)contacting the polypeptide of any of claims 13, 14, 15, or 56 with acompound; and (b) determining the extent of binding of the B7-Lpolypeptide to the compound.
 52. The method of claim 51, furthercomprising determining the activity of the polypeptide when bound to thecompound.
 53. A method of modulating levels of a polypeptide in ananimal comprising administering to the animal the nucleic acid moleculeof any of claims 1, 2, or
 3. 54. A transgenic non-human mammalcomprising the nucleic acid molecule of any of claims 1, 2, or
 3. 55. Aprocess for determining whether a compound inhibits B7-L polypeptideactivity or B7-L polypeptide production comprising exposing a transgenicmammal according to claim 54 to the compound, and measuring B7-Lpolypeptide activity or B7-L polypeptide production in said mammal. 56.An isolated polypeptide comprising the amino acid sequence as set forthin SEQ ID NO: 2 with at least one conservative amino acid substitutionselected from the group consisting of: valine at position 4; isoleucineor valine at position 6; leucine or valine at position 7; methionine orvaline at position 8; isoleucine at position 10; leucine or valine atposition 17; glycine at position 19; serine at position 22; leucine atposition 23; aspartic acid at position 28; leucine or valine at position31; valine at position 32; isoleucine at position 40; leucine atposition 50; valine at position 52; valine, leucine, or methionine atposition 55; arginine at position 61; methionine at position 62; lysineat position 70; serine at position 74; isoleucine or methionine atposition 75; valine at position 76; aspartic acid at position 78;methionine or isoleucine at position 80; arginine at position 84;leucine at position 89; asparagine at position 91; isoleucine or leucineat position 92; isoleucine or leucine at position 94; glutamic acid atposition 96; aspartic acid at position 97; phenylalanine at position100; valine at position 104; leucine at position 105; arginine atposition 107; tyrosine at position 110; glutamic acid at position 111;valine or isoleucine at position 115; serine at position 116; valine atposition 117; glycine at position 121; valine or methionine at position126; valine or isoleucine at position 131; isoleucine or leucine atposition 139; isoleucine at position 141; serine at position 146;phenylalanine at position 148; isoleucine, methionine, or leucine atposition 153; isoleucine at position 160; threonine at position 165;aspartic acid at position 171; phenylalanine at position 174; serine atposition 177; threonine at position 178; valine at position 180;methionine, valine, or isoleucine at position 182; arginine at position183; lysine at position 188; isoleucine or leucine at position 193;lysine at position 200; valine at position 202; isoleucine at position204; valine or methionine at position 209; isoleucine at position 213;isoleucine or valine at position 222; valine at position 223; leucine atposition 225; valine or leucine at position 227; leucine or valine atposition 231; leucine at position 232; valine or leucine at position235; methionine or isoleucine at position 240; arginine at position 250;arginine at position 255; glutamic acid at position 256; serine atposition 264; arginine at position 266; and leucine at position 268;wherein the polypeptide has an activity of the polypeptide as set forthin SEQ ID NO:
 2. 57. A nucleic acid molecule of any of claims 1, 2, or 3attached to a solid support.
 58. An array of nucleic acid moleculescomprising at least one nucleic acid molecule of any of claims 1, 2, or3.